We first took unrelated female subjects from the UK Biobank study. Then we selected and derived 9 classical risk factors including age, parity, age at first birth, alcohol, height, BMI, age at menopause (for post-menopause women), age at menarche, and use of oral contraceptive pill. There was no information on breast cancer family history and so we did not include it into the mode. In addition, for post-menopause women, we included HRT use. We also included the top 10 PCs (code 22009). All the data was extracted from /dcl01/arking/data/UK_Biobank/static/Phenotype/Downloads/tab_delim/ukb45830.tab and /dcl01/arking/data/UK_Biobank/active/pheno/ukbPheno_032022.rds. Age at menopause was extracted from DNAnexus as it was not found in the above two files.
For breast cancer data, we used ICD9 (code 40013) and ICD10 (code 40006) in UK Biobank data. To find incident breast cancer data, we compared the age at cancer diagnosis (code 40008) with the age at recruitment. In particular, from previous publications, bilateral breast cancer and breast cancer in situ (stage 0 breast cancer) should be excluded from the study. There was no information on bilateral breast cancer and given that they are highly rare, we only excluded breast cancer in situ. For this work, we used incident breast cancer patients.
Next we selected geographical data and social economic data. The assessment centre at which a participant consented was assigned a numerical code (field 54 in the UK Biobank data). In analyses adjusted for assessment centre, these codes were treated as factor variables. Participants who were born in the United Kingdom were asked to name their place of birth during a verbal interview at study assessment centres. These answers were used to derive approximate North and East co-ordinates (rounded values, recorded on a metre grid scale from an origin South-West of the UK, fields 129 and 130 in the UK Biobank data). Values less than zero were coded as missing for both variables (Haworth et al. Nature Communications 2019). We also selected education data and household-income to include in the study.
#For our analysis, select: 1. european; 2. post-menopause/pre-menopause; 3. age by category; 4. see the complete dataset (no NA) number; 5. incident cancer cases
dat0=dat0[which(dat0$race=="White"),]
table(dat0$breast_cancer) # 0 is control; 1 is breast cancer; 2 is breast cancer in situ
##
## 0 1 2
## 193511 10681 1802
#add age by category
dat0$agegroups<-cut(dat0$age, breaks=c( 40, 50,60,70,80), right = FALSE)
table(dat0$oral.contraceptive.ever)
##
## -1 -3 0 1
## 213 201 36372 169206
dat0$oral.contraceptive.ever[which(dat0$oral.contraceptive.ever=="-3" | dat0$oral.contraceptive.ever=="-1")]=NA
dat0$age.start.oc[which(dat0$age.start.oc=="-3" | dat0$age.start.oc=="-1")]=NA
dat0$age.last.oc[which(dat0$age.last.oc=="-3" | dat0$age.last.oc=="-1")]=NA
dat0$oral.contraceptive.current=dat0$oral.contraceptive.ever
dat0$oral.contraceptive.current[which(dat0$age.last.oc=="-11")]="current"
dat0$oral.contraceptive.current[which(dat0$oral.contraceptive.current=="0")]="never"
dat0$oral.contraceptive.current[which(dat0$oral.contraceptive.current=="1")]="former"
dat0$age.last.oc[which(dat0$age.last.oc=="-11")]=dat0$age[which(dat0$age.last.oc=="-11")]
dat0$length.oc=as.numeric(as.character(dat0$age.last.oc))-as.numeric(as.character(dat0$age.start.oc))
dat0$length.oc[which(dat0$oral.contraceptive.ever==0)]=0
dat0$oc.cate=NA
dat0$oc.cate[which(dat0$oral.contraceptive.ever==0 | dat0$length.oc<10)]=0
dat0$oc.cate[which( dat0$length.oc>=10)]=1
table(dat0$menopause,dat0$breast_cancer)
##
## 0 1 2
## No 45964 1097 268
## Yes 116965 7881 1289
## Hysterectomy 22242 1144 198
table(dat0$menopause,dat0$breast_cancer,dat0$breast_cancer_incident)
## , , = 0
##
##
## 0 1 2
## No 45964 245 74
## Yes 116965 5219 783
## Hysterectomy 22242 675 112
##
## , , = 1
##
##
## 0 1 2
## No 0 852 194
## Yes 0 2662 506
## Hysterectomy 0 469 86
dat0=dat0[which(dat0$breast_cancer!=2),] #exclude in situ bc
dat0=dat0[-which(dat0$breast_cancer==1 & dat0$breast_cancer_incident!=1),] #exclude non-incident bc
We used the PRS calculator provided by PGSCatalog based on 313 SNPs (Polygenic Score (PGS) ID: PGS000004). The genome build is hg19. After matching with our data and data cleaning, 276 SNPs were used for the calculation. The OR per SD change for breast cancer in UKBiobank is 1.58 for all women; 1.56 for post-menopause women and 1.63 for pre-menopause women. This result is close to the reported OR 1.61 in the manuscript by Mavaddat N et al. Am J Hum Genet (2018).
dat0$prs_scaled=scale(dat0$prs_bc,center = T,scale = T)
fit <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10, data=dat0,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10, family = binomial(),
## data = dat0, model = FALSE, x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.5354 -0.2269 -0.1943 -0.1668 3.2774
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.997383 0.054401 -73.480 <2e-16 ***
## prs_scaled 0.454500 0.015714 28.922 <2e-16 ***
## PC1 -0.006366 0.005225 -1.218 0.2232
## PC2 -0.005165 0.005085 -1.016 0.3097
## PC3 -0.003332 0.006609 -0.504 0.6141
## PC4 -0.001378 0.003423 -0.403 0.6872
## PC5 0.003738 0.002162 1.729 0.0838 .
## PC6 -0.012590 0.006796 -1.853 0.0639 .
## PC7 -0.004379 0.003746 -1.169 0.2424
## PC8 -0.001246 0.004842 -0.257 0.7970
## PC9 -0.005860 0.003388 -1.730 0.0837 .
## PC10 0.005301 0.006622 0.800 0.4235
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 40433 on 197680 degrees of freedom
## Residual deviance: 39579 on 197669 degrees of freedom
## AIC: 39603
##
## Number of Fisher Scoring iterations: 7
exp(0.4545)
## [1] 1.575385
dat0_postmeno_bc=dat0[which(dat0$menopause=="Yes" ),]
table(dat0_postmeno_bc$breast_cancer)
##
## 0 1
## 116965 2662
dat0_postmeno_bc$prs_scaled=scale(dat0_postmeno_bc$prs_bc,center = T,scale = T)
fit <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10, data=dat0_postmeno_bc,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10, family = binomial(),
## data = dat0_postmeno_bc, model = FALSE, x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.7087 -0.2333 -0.2000 -0.1731 3.2468
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.934293 0.072114 -54.557 <2e-16 ***
## prs_scaled 0.441668 0.019705 22.415 <2e-16 ***
## PC1 -0.006631 0.007031 -0.943 0.3457
## PC2 -0.008839 0.006483 -1.363 0.1727
## PC3 -0.007072 0.008211 -0.861 0.3891
## PC4 -0.001218 0.004379 -0.278 0.7810
## PC5 0.004617 0.002699 1.710 0.0872 .
## PC6 -0.015641 0.008785 -1.780 0.0750 .
## PC7 -0.008708 0.004858 -1.793 0.0730 .
## PC8 0.003905 0.006221 0.628 0.5302
## PC9 -0.007549 0.004138 -1.824 0.0681 .
## PC10 0.008745 0.008448 1.035 0.3006
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 25524 on 119626 degrees of freedom
## Residual deviance: 25003 on 119615 degrees of freedom
## AIC: 25027
##
## Number of Fisher Scoring iterations: 7
exp(0.441668)
## [1] 1.555299
colnames(dat0_postmeno_bc)[7]="age.menarche"
dat0_postmeno_bc$n.children=as.numeric(as.character(dat0_postmeno_bc$n.children))
dat0_postmeno_bc$age.menopause=as.numeric(as.character(dat0_postmeno_bc$age.menopause))
dat0_postmeno_bc$n.children[which(dat0_postmeno_bc$n.children=="-3")]=NA
#winsorization
dat0_postmeno_bc$n.children.win=dat0_postmeno_bc$n.children
dat0_postmeno_bc$n.children.win[which(dat0_postmeno_bc$n.children.win>=5)]=5
dat0_postmeno_bc$alcohol=NA
dat0_postmeno_bc$alcohol[which(dat0_postmeno_bc$AlcoholFreq=="Never" | dat0_postmeno_bc$AlcoholFreq== "Special occasions only")]=0
dat0_postmeno_bc$alcohol[which(dat0_postmeno_bc$AlcoholFreq=="Daily or almost daily" | dat0_postmeno_bc$AlcoholFreq== "Three or four times a week" |
dat0_postmeno_bc$AlcoholFreq== "Once or twice a week" | dat0_postmeno_bc$AlcoholFreq=="One to three times a month" )]=1
dat0_postmeno_bc$age.firstbirth=as.numeric(as.character(dat0_postmeno_bc$age.firstbirth))
dat0_postmeno_bc$age.firstbirth[which(dat0_postmeno_bc$age.firstbirth== -3 | dat0_postmeno_bc$age.firstbirth== -4)]=NA
dat0_postmeno_bc$age.firstbirth[which(dat0_postmeno_bc$n.children==0)]=999
dat0_postmeno_bc$age.firstbirth.group=NA
dat0_postmeno_bc$age.firstbirth.group<-cut(dat0_postmeno_bc$age.firstbirth, breaks=c( 0, 25,35,80,1000), right = FALSE)
dat0_postmeno_bc$age.menarche[which(dat0_postmeno_bc$age.menarche<0)]=NA
dat0_postmeno_bc$birth.x[which(dat0_postmeno_bc$birth.x<0)]=NA
dat0_postmeno_bc$birth.y[which(dat0_postmeno_bc$birth.y<0)]=NA
#For post-menopause women, let's add the HRT use
hrt=hrt[-1,]
colnames(hrt)=c("IID","HRT.ever","age.start.hrt","age.last.hrt")
dat0_postmeno_bc=merge(dat0_postmeno_bc,hrt,by="IID")
dat0_postmeno_bc$HRT.ever[which(dat0_postmeno_bc$HRT.ever=="-3" | dat0_postmeno_bc$HRT.ever=="-1")]=NA
dat0_postmeno_bc$age.start.hrt[which(dat0_postmeno_bc$age.start.hrt=="-3" | dat0_postmeno_bc$age.start.hrt=="-1")]=NA
dat0_postmeno_bc$age.last.hrt[which(dat0_postmeno_bc$age.last.hrt=="-3" | dat0_postmeno_bc$age.last.hrt=="-1")]=NA
dat0_postmeno_bc$age.last.hrt[which(dat0_postmeno_bc$age.last.hrt=="-11")]=dat0_postmeno_bc$age[which(dat0_postmeno_bc$age.last.hrt=="-11")]
dat0_postmeno_bc$length.hrt=as.numeric(as.character(dat0_postmeno_bc$age.last.hrt))-as.numeric(as.character(dat0_postmeno_bc$age.start.hrt))
dat0_postmeno_bc$length.hrt[which(dat0_postmeno_bc$HRT.ever==0)]=0
summary(dat0_postmeno_bc$length.hrt)
## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
## 0.000 0.000 0.000 2.903 5.000 45.000 7667
table(dat0_postmeno_bc$HRT.ever) #let's just include HRT use: ever/never
##
## 0 1
## 62090 57280
We first look at post-menopause women:
dat_test=dat0_postmeno_bc[,c("IID","prs_bc","age","age.menarche","BMI","height","n.children.win","age.firstbirth",
"breast_cancer","breast_cancer_incident","length.oc","oral.contraceptive.ever",
"assessment_center","age.menopause","agegroups", "HRT.ever",
"oc.cate" ,"alcohol","age.firstbirth.group","PC1","PC2","PC3","PC4","PC5","PC6","PC7","PC8","PC9","PC10")]
dat_test=dat_test[complete.cases(dat_test),]
table(dat_test$breast_cancer)
##
## 0 1
## 97383 2217
table(dat_test$breast_cancer_incident)
##
## 0 1
## 97383 2217
dim(dat_test)
## [1] 99600 29
dat_test$prs_scaled=scale(dat_test$prs_bc,center = T,scale = T)
dat_test$age.scale=scale(dat_test$age,center = T,scale=T)
dat_test$age.menarche.scale=scale(dat_test$age.menarche,center = T,scale=T)
dat_test$age.menopause.scale=scale(dat_test$age.menopause,center = T,scale=T)
dat_test$n.children.scale=scale(dat_test$n.children.win,center=T,scale = T)
dat_test$height.scale=scale(dat_test$height,center=T,scale = T)
dat_test$BMI.scale=scale(dat_test$BMI,center=T,scale = T)
dat_test$length.oc.scale=scale(dat_test$length.oc,center=T,scale = T)
dat_location=dat0_postmeno_bc[,c("IID","birth.x","birth.y")]
dat_test=merge(dat_test,dat_location,by="IID")
dat_test$birth.x=scale(dat_test$birth.x,center=T,scale=T)
dat_test$birth.y=scale(dat_test$birth.y,center=T,scale=T)
#add oc category
dat_test$oc.cate2=NA
dat_test$oc.cate2[which(dat_test$oral.contraceptive.ever==0)]=0
dat_test$oc.cate2[which(dat_test$oral.contraceptive.ever==1 & dat_test$length.oc<10)]=1
dat_test$oc.cate2[which( dat_test$length.oc>=10)]=2
#more specified interval
dat_test$oc.cate3=NA
dat_test$oc.cate3[which(dat_test$oral.contraceptive.ever==0)]=0
dat_test$oc.cate3[which(dat_test$oral.contraceptive.ever==1 & dat_test$length.oc<5)]=1
dat_test$oc.cate3[which( dat_test$length.oc>=5 & dat_test$length.oc < 10)]=2
dat_test$oc.cate3[which( dat_test$length.oc>=10 & dat_test$length.oc < 15)]=3
dat_test$oc.cate3[which( dat_test$length.oc>=15 )]=4
dat_test_complete=dat_test[complete.cases(dat_test),]
table(dat_test_complete$breast_cancer)
##
## 0 1
## 89241 2024
fit.int.all <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+length.oc.scale+BMI.scale+relevel(factor(dat_test_complete$assessment_center),ref = "11001")+alcohol+prs_scaled:HRT.ever+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:length.oc.scale+prs_scaled:age.menopause.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group, data=dat_test_complete,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit.int.all)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10 + HRT.ever + agegroups +
## n.children.scale + birth.x + birth.y + age.firstbirth.group +
## height.scale + age.menarche.scale + age.menopause.scale +
## length.oc.scale + BMI.scale + relevel(factor(dat_test_complete$assessment_center),
## ref = "11001") + alcohol + prs_scaled:HRT.ever + prs_scaled:birth.x +
## prs_scaled:birth.y + prs_scaled:length.oc.scale + prs_scaled:age.menopause.scale +
## prs_scaled:age.menarche.scale + prs_scaled:BMI.scale + prs_scaled:agegroups +
## prs_scaled:alcohol + prs_scaled:height.scale + prs_scaled:n.children.scale +
## prs_scaled:age.firstbirth.group, family = binomial(), data = dat_test_complete,
## model = FALSE, x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.0288 -0.2357 -0.1951 -0.1590 3.6439
##
## Coefficients:
## Estimate
## (Intercept) -4.378e+00
## prs_scaled 5.483e-01
## PC1 -2.484e-03
## PC2 -1.197e-02
## PC3 -2.847e-03
## PC4 2.158e-03
## PC5 2.129e-03
## PC6 -1.818e-02
## PC7 -4.929e-03
## PC8 1.020e-02
## PC9 -7.407e-03
## PC10 7.823e-04
## HRT.ever1 1.321e-01
## agegroups[50,60) 4.504e-01
## agegroups[60,70) 6.826e-01
## agegroups[70,80) 8.795e-01
## n.children.scale -7.809e-02
## birth.x 3.131e-02
## birth.y 1.438e-02
## age.firstbirth.group[25,35) 1.358e-02
## age.firstbirth.group[35,80) 2.584e-01
## age.firstbirth.group[80,1e+03) -3.042e-03
## height.scale 1.345e-01
## age.menarche.scale -1.617e-02
## age.menopause.scale 9.678e-02
## length.oc.scale 2.577e-02
## BMI.scale 1.476e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 4.230e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 -1.246e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 -3.593e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 -2.197e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 -2.079e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 -1.473e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 -1.294e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 -2.089e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 -3.011e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 -4.446e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -3.394e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -2.830e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -4.061e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -6.837e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -2.225e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -4.738e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -7.266e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -5.464e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -5.708e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -2.962e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -1.220e+01
## alcohol 1.935e-01
## prs_scaled:HRT.ever1 -9.527e-03
## prs_scaled:birth.x -6.816e-02
## prs_scaled:birth.y -1.195e-02
## prs_scaled:length.oc.scale -5.475e-02
## prs_scaled:age.menopause.scale -2.037e-03
## prs_scaled:age.menarche.scale -9.776e-03
## prs_scaled:BMI.scale -9.503e-03
## prs_scaled:agegroups[50,60) -5.049e-02
## prs_scaled:agegroups[60,70) -5.481e-02
## prs_scaled:agegroups[70,80) -5.449e-01
## prs_scaled:alcohol -9.063e-02
## prs_scaled:height.scale -2.033e-02
## prs_scaled:n.children.scale 5.335e-03
## prs_scaled:age.firstbirth.group[25,35) 1.075e-01
## prs_scaled:age.firstbirth.group[35,80) -8.304e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -1.906e-02
## Std. Error
## (Intercept) 2.559e-01
## prs_scaled 1.942e-01
## PC1 8.037e-03
## PC2 7.287e-03
## PC3 9.693e-03
## PC4 5.534e-03
## PC5 3.872e-03
## PC6 1.247e-02
## PC7 7.379e-03
## PC8 8.854e-03
## PC9 5.797e-03
## PC10 1.081e-02
## HRT.ever1 5.067e-02
## agegroups[50,60) 2.018e-01
## agegroups[60,70) 2.023e-01
## agegroups[70,80) 3.551e-01
## n.children.scale 3.976e-02
## birth.x 3.350e-02
## birth.y 3.947e-02
## age.firstbirth.group[25,35) 5.861e-02
## age.firstbirth.group[35,80) 1.170e-01
## age.firstbirth.group[80,1e+03) 1.119e-01
## height.scale 2.557e-02
## age.menarche.scale 2.511e-02
## age.menopause.scale 2.648e-02
## length.oc.scale 2.520e-02
## BMI.scale 2.384e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 7.319e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 1.757e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 1.809e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 1.756e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 1.729e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 1.673e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 1.529e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 1.538e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 1.534e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 1.489e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 1.504e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 2.042e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 1.541e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 1.640e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 1.498e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 1.733e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 1.794e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 1.721e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 1.713e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 3.381e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 1.281e+02
## alcohol 6.354e-02
## prs_scaled:HRT.ever1 4.650e-02
## prs_scaled:birth.x 2.478e-02
## prs_scaled:birth.y 2.496e-02
## prs_scaled:length.oc.scale 2.338e-02
## prs_scaled:age.menopause.scale 2.427e-02
## prs_scaled:age.menarche.scale 2.317e-02
## prs_scaled:BMI.scale 2.182e-02
## prs_scaled:agegroups[50,60) 1.879e-01
## prs_scaled:agegroups[60,70) 1.880e-01
## prs_scaled:agegroups[70,80) 3.504e-01
## prs_scaled:alcohol 5.702e-02
## prs_scaled:height.scale 2.329e-02
## prs_scaled:n.children.scale 3.628e-02
## prs_scaled:age.firstbirth.group[25,35) 5.358e-02
## prs_scaled:age.firstbirth.group[35,80) 1.108e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 1.034e-01
## z value
## (Intercept) -17.108
## prs_scaled 2.823
## PC1 -0.309
## PC2 -1.642
## PC3 -0.294
## PC4 0.390
## PC5 0.550
## PC6 -1.458
## PC7 -0.668
## PC8 1.152
## PC9 -1.278
## PC10 0.072
## HRT.ever1 2.608
## agegroups[50,60) 2.232
## agegroups[60,70) 3.375
## agegroups[70,80) 2.477
## n.children.scale -1.964
## birth.x 0.935
## birth.y 0.364
## age.firstbirth.group[25,35) 0.232
## age.firstbirth.group[35,80) 2.209
## age.firstbirth.group[80,1e+03) -0.027
## height.scale 5.260
## age.menarche.scale -0.644
## age.menopause.scale 3.655
## length.oc.scale 1.023
## BMI.scale 6.191
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.058
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 -0.709
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 -1.986
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 -1.252
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 -1.202
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 -0.880
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 -0.846
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 -1.358
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 -1.962
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 -2.986
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -2.257
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -1.386
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -2.635
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -4.170
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -1.486
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -2.735
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -4.051
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -3.175
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -3.332
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -0.876
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -0.095
## alcohol 3.046
## prs_scaled:HRT.ever1 -0.205
## prs_scaled:birth.x -2.751
## prs_scaled:birth.y -0.479
## prs_scaled:length.oc.scale -2.342
## prs_scaled:age.menopause.scale -0.084
## prs_scaled:age.menarche.scale -0.422
## prs_scaled:BMI.scale -0.436
## prs_scaled:agegroups[50,60) -0.269
## prs_scaled:agegroups[60,70) -0.292
## prs_scaled:agegroups[70,80) -1.555
## prs_scaled:alcohol -1.590
## prs_scaled:height.scale -0.873
## prs_scaled:n.children.scale 0.147
## prs_scaled:age.firstbirth.group[25,35) 2.007
## prs_scaled:age.firstbirth.group[35,80) -0.749
## prs_scaled:age.firstbirth.group[80,1e+03) -0.184
## Pr(>|z|)
## (Intercept) < 2e-16
## prs_scaled 0.004757
## PC1 0.757272
## PC2 0.100499
## PC3 0.768997
## PC4 0.696612
## PC5 0.582335
## PC6 0.144805
## PC7 0.504178
## PC8 0.249177
## PC9 0.201315
## PC10 0.942316
## HRT.ever1 0.009119
## agegroups[50,60) 0.025614
## agegroups[60,70) 0.000738
## agegroups[70,80) 0.013265
## n.children.scale 0.049507
## birth.x 0.349976
## birth.y 0.715600
## age.firstbirth.group[25,35) 0.816759
## age.firstbirth.group[35,80) 0.027177
## age.firstbirth.group[80,1e+03) 0.978315
## height.scale 1.44e-07
## age.menarche.scale 0.519605
## age.menopause.scale 0.000257
## length.oc.scale 0.306482
## BMI.scale 5.99e-10
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.953905
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.478222
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 0.047039
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.210722
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.229349
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 0.378607
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.397484
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 0.174354
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.049713
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.002825
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 0.024034
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 0.165714
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 0.008414
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 3.05e-05
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 0.137305
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 0.006247
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 5.11e-05
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 0.001496
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 0.000863
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 0.380954
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 0.924079
## alcohol 0.002318
## prs_scaled:HRT.ever1 0.837672
## prs_scaled:birth.x 0.005944
## prs_scaled:birth.y 0.631928
## prs_scaled:length.oc.scale 0.019202
## prs_scaled:age.menopause.scale 0.933098
## prs_scaled:age.menarche.scale 0.673135
## prs_scaled:BMI.scale 0.663127
## prs_scaled:agegroups[50,60) 0.788086
## prs_scaled:agegroups[60,70) 0.770590
## prs_scaled:agegroups[70,80) 0.119929
## prs_scaled:alcohol 0.111927
## prs_scaled:height.scale 0.382744
## prs_scaled:n.children.scale 0.883102
## prs_scaled:age.firstbirth.group[25,35) 0.044761
## prs_scaled:age.firstbirth.group[35,80) 0.453575
## prs_scaled:age.firstbirth.group[80,1e+03) 0.853733
##
## (Intercept) ***
## prs_scaled **
## PC1
## PC2
## PC3
## PC4
## PC5
## PC6
## PC7
## PC8
## PC9
## PC10
## HRT.ever1 **
## agegroups[50,60) *
## agegroups[60,70) ***
## agegroups[70,80) *
## n.children.scale *
## birth.x
## birth.y
## age.firstbirth.group[25,35)
## age.firstbirth.group[35,80) *
## age.firstbirth.group[80,1e+03)
## height.scale ***
## age.menarche.scale
## age.menopause.scale ***
## length.oc.scale
## BMI.scale ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 *
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 *
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 *
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023
## alcohol **
## prs_scaled:HRT.ever1
## prs_scaled:birth.x **
## prs_scaled:birth.y
## prs_scaled:length.oc.scale *
## prs_scaled:age.menopause.scale
## prs_scaled:age.menarche.scale
## prs_scaled:BMI.scale
## prs_scaled:agegroups[50,60)
## prs_scaled:agegroups[60,70)
## prs_scaled:agegroups[70,80)
## prs_scaled:alcohol
## prs_scaled:height.scale
## prs_scaled:n.children.scale
## prs_scaled:age.firstbirth.group[25,35) *
## prs_scaled:age.firstbirth.group[35,80)
## prs_scaled:age.firstbirth.group[80,1e+03)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 19420 on 91264 degrees of freedom
## Residual deviance: 18772 on 91200 degrees of freedom
## AIC: 18902
##
## Number of Fisher Scoring iterations: 14
fit.int.all2 <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+factor(oc.cate2)+BMI.scale+relevel(factor(dat_test_complete$assessment_center),ref = "11001")+alcohol+prs_scaled:HRT.ever+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:factor(oc.cate2)+prs_scaled:age.menopause.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group, data=dat_test_complete,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit.int.all2)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10 + HRT.ever + agegroups +
## n.children.scale + birth.x + birth.y + age.firstbirth.group +
## height.scale + age.menarche.scale + age.menopause.scale +
## factor(oc.cate2) + BMI.scale + relevel(factor(dat_test_complete$assessment_center),
## ref = "11001") + alcohol + prs_scaled:HRT.ever + prs_scaled:birth.x +
## prs_scaled:birth.y + prs_scaled:factor(oc.cate2) + prs_scaled:age.menopause.scale +
## prs_scaled:age.menarche.scale + prs_scaled:BMI.scale + prs_scaled:agegroups +
## prs_scaled:alcohol + prs_scaled:height.scale + prs_scaled:n.children.scale +
## prs_scaled:age.firstbirth.group, family = binomial(), data = dat_test_complete,
## model = FALSE, x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.0419 -0.2358 -0.1950 -0.1590 3.6054
##
## Coefficients:
## Estimate
## (Intercept) -4.399e+00
## prs_scaled 6.514e-01
## PC1 -2.376e-03
## PC2 -1.192e-02
## PC3 -2.837e-03
## PC4 2.191e-03
## PC5 2.048e-03
## PC6 -1.838e-02
## PC7 -5.053e-03
## PC8 1.019e-02
## PC9 -7.452e-03
## PC10 7.298e-04
## HRT.ever1 1.321e-01
## agegroups[50,60) 4.525e-01
## agegroups[60,70) 6.806e-01
## agegroups[70,80) 8.736e-01
## n.children.scale -7.847e-02
## birth.x 3.130e-02
## birth.y 1.441e-02
## age.firstbirth.group[25,35) 1.372e-02
## age.firstbirth.group[35,80) 2.560e-01
## age.firstbirth.group[80,1e+03) -4.469e-03
## height.scale 1.348e-01
## age.menarche.scale -1.628e-02
## age.menopause.scale 9.765e-02
## factor(oc.cate2)1 -1.431e-03
## factor(oc.cate2)2 5.455e-02
## BMI.scale 1.475e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 4.509e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 -1.228e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 -3.541e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 -2.156e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 -2.043e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 -1.459e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 -1.241e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 -2.083e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 -2.965e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 -4.415e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -3.366e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -2.790e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -4.028e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -6.795e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -2.179e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -4.693e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -7.217e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -5.421e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -5.684e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -2.881e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -1.220e+01
## alcohol 1.945e-01
## prs_scaled:HRT.ever1 -2.706e-03
## prs_scaled:birth.x -6.820e-02
## prs_scaled:birth.y -1.191e-02
## prs_scaled:factor(oc.cate2)1 -8.747e-02
## prs_scaled:factor(oc.cate2)2 -1.803e-01
## prs_scaled:age.menopause.scale -2.116e-03
## prs_scaled:age.menarche.scale -1.011e-02
## prs_scaled:BMI.scale -9.218e-03
## prs_scaled:agegroups[50,60) -5.346e-02
## prs_scaled:agegroups[60,70) -6.641e-02
## prs_scaled:agegroups[70,80) -5.695e-01
## prs_scaled:alcohol -8.739e-02
## prs_scaled:height.scale -1.939e-02
## prs_scaled:n.children.scale 4.587e-03
## prs_scaled:age.firstbirth.group[25,35) 1.085e-01
## prs_scaled:age.firstbirth.group[35,80) -8.207e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -3.010e-02
## Std. Error
## (Intercept) 2.606e-01
## prs_scaled 1.996e-01
## PC1 8.018e-03
## PC2 7.278e-03
## PC3 9.695e-03
## PC4 5.534e-03
## PC5 3.871e-03
## PC6 1.247e-02
## PC7 7.377e-03
## PC8 8.855e-03
## PC9 5.796e-03
## PC10 1.081e-02
## HRT.ever1 5.081e-02
## agegroups[50,60) 2.018e-01
## agegroups[60,70) 2.023e-01
## agegroups[70,80) 3.556e-01
## n.children.scale 3.974e-02
## birth.x 3.350e-02
## birth.y 3.948e-02
## age.firstbirth.group[25,35) 5.862e-02
## age.firstbirth.group[35,80) 1.170e-01
## age.firstbirth.group[80,1e+03) 1.122e-01
## height.scale 2.557e-02
## age.menarche.scale 2.511e-02
## age.menopause.scale 2.647e-02
## factor(oc.cate2)1 6.653e-02
## factor(oc.cate2)2 6.972e-02
## BMI.scale 2.384e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 7.318e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 1.758e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 1.810e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 1.756e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 1.730e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 1.674e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 1.529e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 1.538e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 1.535e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 1.489e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 1.504e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 2.042e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 1.541e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 1.640e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 1.498e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 1.733e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 1.794e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 1.721e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 1.714e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 3.382e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 1.280e+02
## alcohol 6.364e-02
## prs_scaled:HRT.ever1 4.670e-02
## prs_scaled:birth.x 2.477e-02
## prs_scaled:birth.y 2.495e-02
## prs_scaled:factor(oc.cate2)1 6.018e-02
## prs_scaled:factor(oc.cate2)2 6.370e-02
## prs_scaled:age.menopause.scale 2.428e-02
## prs_scaled:age.menarche.scale 2.318e-02
## prs_scaled:BMI.scale 2.181e-02
## prs_scaled:agegroups[50,60) 1.877e-01
## prs_scaled:agegroups[60,70) 1.880e-01
## prs_scaled:agegroups[70,80) 3.505e-01
## prs_scaled:alcohol 5.706e-02
## prs_scaled:height.scale 2.331e-02
## prs_scaled:n.children.scale 3.622e-02
## prs_scaled:age.firstbirth.group[25,35) 5.359e-02
## prs_scaled:age.firstbirth.group[35,80) 1.108e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 1.037e-01
## z value
## (Intercept) -16.881
## prs_scaled 3.264
## PC1 -0.296
## PC2 -1.638
## PC3 -0.293
## PC4 0.396
## PC5 0.529
## PC6 -1.474
## PC7 -0.685
## PC8 1.151
## PC9 -1.286
## PC10 0.068
## HRT.ever1 2.600
## agegroups[50,60) 2.242
## agegroups[60,70) 3.364
## agegroups[70,80) 2.457
## n.children.scale -1.975
## birth.x 0.934
## birth.y 0.365
## age.firstbirth.group[25,35) 0.234
## age.firstbirth.group[35,80) 2.188
## age.firstbirth.group[80,1e+03) -0.040
## height.scale 5.271
## age.menarche.scale -0.648
## age.menopause.scale 3.689
## factor(oc.cate2)1 -0.022
## factor(oc.cate2)2 0.782
## BMI.scale 6.189
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.062
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 -0.699
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 -1.957
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 -1.228
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 -1.181
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 -0.872
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 -0.812
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 -1.354
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 -1.932
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 -2.965
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -2.238
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -1.366
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -2.613
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -4.143
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -1.455
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -2.708
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -4.023
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -3.150
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -3.317
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -0.852
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -0.095
## alcohol 3.057
## prs_scaled:HRT.ever1 -0.058
## prs_scaled:birth.x -2.753
## prs_scaled:birth.y -0.477
## prs_scaled:factor(oc.cate2)1 -1.454
## prs_scaled:factor(oc.cate2)2 -2.831
## prs_scaled:age.menopause.scale -0.087
## prs_scaled:age.menarche.scale -0.436
## prs_scaled:BMI.scale -0.423
## prs_scaled:agegroups[50,60) -0.285
## prs_scaled:agegroups[60,70) -0.353
## prs_scaled:agegroups[70,80) -1.625
## prs_scaled:alcohol -1.532
## prs_scaled:height.scale -0.832
## prs_scaled:n.children.scale 0.127
## prs_scaled:age.firstbirth.group[25,35) 2.025
## prs_scaled:age.firstbirth.group[35,80) -0.741
## prs_scaled:age.firstbirth.group[80,1e+03) -0.290
## Pr(>|z|)
## (Intercept) < 2e-16
## prs_scaled 0.001099
## PC1 0.766954
## PC2 0.101385
## PC3 0.769777
## PC4 0.692118
## PC5 0.596743
## PC6 0.140597
## PC7 0.493348
## PC8 0.249870
## PC9 0.198503
## PC10 0.946171
## HRT.ever1 0.009322
## agegroups[50,60) 0.024948
## agegroups[60,70) 0.000769
## agegroups[70,80) 0.014025
## n.children.scale 0.048276
## birth.x 0.350219
## birth.y 0.715144
## age.firstbirth.group[25,35) 0.814899
## age.firstbirth.group[35,80) 0.028680
## age.firstbirth.group[80,1e+03) 0.968225
## height.scale 1.36e-07
## age.menarche.scale 0.516666
## age.menopause.scale 0.000225
## factor(oc.cate2)1 0.982843
## factor(oc.cate2)2 0.433962
## BMI.scale 6.05e-10
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.950865
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.484689
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 0.050369
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.219561
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.237591
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 0.383427
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.416867
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 0.175688
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.053395
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.003030
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 0.025236
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 0.171944
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 0.008975
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 3.43e-05
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 0.145758
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 0.006777
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 5.74e-05
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 0.001634
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 0.000910
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 0.394244
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 0.924037
## alcohol 0.002237
## prs_scaled:HRT.ever1 0.953796
## prs_scaled:birth.x 0.005896
## prs_scaled:birth.y 0.633206
## prs_scaled:factor(oc.cate2)1 0.146083
## prs_scaled:factor(oc.cate2)2 0.004646
## prs_scaled:age.menopause.scale 0.930534
## prs_scaled:age.menarche.scale 0.662824
## prs_scaled:BMI.scale 0.672614
## prs_scaled:agegroups[50,60) 0.775813
## prs_scaled:agegroups[60,70) 0.723831
## prs_scaled:agegroups[70,80) 0.104243
## prs_scaled:alcohol 0.125628
## prs_scaled:height.scale 0.405475
## prs_scaled:n.children.scale 0.899223
## prs_scaled:age.firstbirth.group[25,35) 0.042848
## prs_scaled:age.firstbirth.group[35,80) 0.458799
## prs_scaled:age.firstbirth.group[80,1e+03) 0.771536
##
## (Intercept) ***
## prs_scaled **
## PC1
## PC2
## PC3
## PC4
## PC5
## PC6
## PC7
## PC8
## PC9
## PC10
## HRT.ever1 **
## agegroups[50,60) *
## agegroups[60,70) ***
## agegroups[70,80) *
## n.children.scale *
## birth.x
## birth.y
## age.firstbirth.group[25,35)
## age.firstbirth.group[35,80) *
## age.firstbirth.group[80,1e+03)
## height.scale ***
## age.menarche.scale
## age.menopause.scale ***
## factor(oc.cate2)1
## factor(oc.cate2)2
## BMI.scale ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 .
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 .
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 *
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023
## alcohol **
## prs_scaled:HRT.ever1
## prs_scaled:birth.x **
## prs_scaled:birth.y
## prs_scaled:factor(oc.cate2)1
## prs_scaled:factor(oc.cate2)2 **
## prs_scaled:age.menopause.scale
## prs_scaled:age.menarche.scale
## prs_scaled:BMI.scale
## prs_scaled:agegroups[50,60)
## prs_scaled:agegroups[60,70)
## prs_scaled:agegroups[70,80)
## prs_scaled:alcohol
## prs_scaled:height.scale
## prs_scaled:n.children.scale
## prs_scaled:age.firstbirth.group[25,35) *
## prs_scaled:age.firstbirth.group[35,80)
## prs_scaled:age.firstbirth.group[80,1e+03)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 19420 on 91264 degrees of freedom
## Residual deviance: 18768 on 91198 degrees of freedom
## AIC: 18902
##
## Number of Fisher Scoring iterations: 14
fit.int.all3 <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+factor(oc.cate3)+BMI.scale+relevel(factor(dat_test_complete$assessment_center),ref = "11001")+alcohol+prs_scaled:birth.x+prs_scaled:HRT.ever+prs_scaled:birth.y+prs_scaled:factor(oc.cate3)+prs_scaled:age.menopause.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group, data=dat_test_complete,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit.int.all3)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10 + HRT.ever + agegroups +
## n.children.scale + birth.x + birth.y + age.firstbirth.group +
## height.scale + age.menarche.scale + age.menopause.scale +
## factor(oc.cate3) + BMI.scale + relevel(factor(dat_test_complete$assessment_center),
## ref = "11001") + alcohol + prs_scaled:birth.x + prs_scaled:HRT.ever +
## prs_scaled:birth.y + prs_scaled:factor(oc.cate3) + prs_scaled:age.menopause.scale +
## prs_scaled:age.menarche.scale + prs_scaled:BMI.scale + prs_scaled:agegroups +
## prs_scaled:alcohol + prs_scaled:height.scale + prs_scaled:n.children.scale +
## prs_scaled:age.firstbirth.group, family = binomial(), data = dat_test_complete,
## model = FALSE, x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.0372 -0.2359 -0.1950 -0.1591 3.6194
##
## Coefficients:
## Estimate
## (Intercept) -4.400e+00
## prs_scaled 6.544e-01
## PC1 -2.371e-03
## PC2 -1.187e-02
## PC3 -2.861e-03
## PC4 2.166e-03
## PC5 2.130e-03
## PC6 -1.831e-02
## PC7 -5.034e-03
## PC8 1.017e-02
## PC9 -7.414e-03
## PC10 6.726e-04
## HRT.ever1 1.312e-01
## agegroups[50,60) 4.520e-01
## agegroups[60,70) 6.835e-01
## agegroups[70,80) 8.768e-01
## n.children.scale -7.760e-02
## birth.x 3.127e-02
## birth.y 1.452e-02
## age.firstbirth.group[25,35) 1.204e-02
## age.firstbirth.group[35,80) 2.558e-01
## age.firstbirth.group[80,1e+03) -2.487e-03
## height.scale 1.348e-01
## age.menarche.scale -1.641e-02
## age.menopause.scale 9.776e-02
## factor(oc.cate3)1 -3.481e-02
## factor(oc.cate3)2 3.667e-02
## factor(oc.cate3)3 6.553e-02
## factor(oc.cate3)4 4.715e-02
## BMI.scale 1.475e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 4.638e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 -1.224e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 -3.538e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 -2.185e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 -2.063e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 -1.459e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 -1.250e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 -2.078e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 -2.969e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 -4.422e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -3.361e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -2.798e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -4.040e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -6.791e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -2.180e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -4.703e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -7.230e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -5.434e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -5.683e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -2.885e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -1.220e+01
## alcohol 1.929e-01
## prs_scaled:birth.x -6.843e-02
## prs_scaled:HRT.ever1 -3.209e-03
## prs_scaled:birth.y -1.242e-02
## prs_scaled:factor(oc.cate3)1 -9.670e-02
## prs_scaled:factor(oc.cate3)2 -7.737e-02
## prs_scaled:factor(oc.cate3)3 -1.564e-01
## prs_scaled:factor(oc.cate3)4 -2.015e-01
## prs_scaled:age.menopause.scale -1.909e-03
## prs_scaled:age.menarche.scale -1.013e-02
## prs_scaled:BMI.scale -9.135e-03
## prs_scaled:agegroups[50,60) -5.656e-02
## prs_scaled:agegroups[60,70) -6.858e-02
## prs_scaled:agegroups[70,80) -5.727e-01
## prs_scaled:alcohol -8.760e-02
## prs_scaled:height.scale -1.911e-02
## prs_scaled:n.children.scale 4.376e-03
## prs_scaled:age.firstbirth.group[25,35) 1.071e-01
## prs_scaled:age.firstbirth.group[35,80) -8.183e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -2.902e-02
## Std. Error
## (Intercept) 2.607e-01
## prs_scaled 1.999e-01
## PC1 8.019e-03
## PC2 7.276e-03
## PC3 9.681e-03
## PC4 5.528e-03
## PC5 3.871e-03
## PC6 1.248e-02
## PC7 7.379e-03
## PC8 8.858e-03
## PC9 5.795e-03
## PC10 1.081e-02
## HRT.ever1 5.082e-02
## agegroups[50,60) 2.019e-01
## agegroups[60,70) 2.025e-01
## agegroups[70,80) 3.557e-01
## n.children.scale 3.976e-02
## birth.x 3.350e-02
## birth.y 3.947e-02
## age.firstbirth.group[25,35) 5.867e-02
## age.firstbirth.group[35,80) 1.170e-01
## age.firstbirth.group[80,1e+03) 1.122e-01
## height.scale 2.558e-02
## age.menarche.scale 2.511e-02
## age.menopause.scale 2.647e-02
## factor(oc.cate3)1 7.581e-02
## factor(oc.cate3)2 7.781e-02
## factor(oc.cate3)3 8.164e-02
## factor(oc.cate3)4 8.012e-02
## BMI.scale 2.384e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 7.319e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 1.758e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 1.810e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 1.756e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 1.730e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 1.674e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 1.529e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 1.538e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 1.535e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 1.489e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 1.504e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 2.042e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 1.542e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 1.640e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 1.498e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 1.733e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 1.794e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 1.721e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 1.714e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 3.382e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 1.280e+02
## alcohol 6.367e-02
## prs_scaled:birth.x 2.477e-02
## prs_scaled:HRT.ever1 4.670e-02
## prs_scaled:birth.y 2.496e-02
## prs_scaled:factor(oc.cate3)1 6.883e-02
## prs_scaled:factor(oc.cate3)2 7.040e-02
## prs_scaled:factor(oc.cate3)3 7.513e-02
## prs_scaled:factor(oc.cate3)4 7.382e-02
## prs_scaled:age.menopause.scale 2.427e-02
## prs_scaled:age.menarche.scale 2.318e-02
## prs_scaled:BMI.scale 2.183e-02
## prs_scaled:agegroups[50,60) 1.880e-01
## prs_scaled:agegroups[60,70) 1.883e-01
## prs_scaled:agegroups[70,80) 3.506e-01
## prs_scaled:alcohol 5.710e-02
## prs_scaled:height.scale 2.331e-02
## prs_scaled:n.children.scale 3.624e-02
## prs_scaled:age.firstbirth.group[25,35) 5.364e-02
## prs_scaled:age.firstbirth.group[35,80) 1.108e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 1.037e-01
## z value
## (Intercept) -16.879
## prs_scaled 3.275
## PC1 -0.296
## PC2 -1.631
## PC3 -0.296
## PC4 0.392
## PC5 0.550
## PC6 -1.468
## PC7 -0.682
## PC8 1.148
## PC9 -1.279
## PC10 0.062
## HRT.ever1 2.582
## agegroups[50,60) 2.239
## agegroups[60,70) 3.376
## agegroups[70,80) 2.465
## n.children.scale -1.952
## birth.x 0.933
## birth.y 0.368
## age.firstbirth.group[25,35) 0.205
## age.firstbirth.group[35,80) 2.186
## age.firstbirth.group[80,1e+03) -0.022
## height.scale 5.272
## age.menarche.scale -0.653
## age.menopause.scale 3.693
## factor(oc.cate3)1 -0.459
## factor(oc.cate3)2 0.471
## factor(oc.cate3)3 0.803
## factor(oc.cate3)4 0.588
## BMI.scale 6.188
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.063
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 -0.696
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 -1.955
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 -1.244
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 -1.192
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 -0.872
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 -0.817
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 -1.351
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 -1.935
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 -2.969
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -2.234
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -1.370
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -2.621
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -4.141
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -1.455
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -2.713
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -4.030
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -3.157
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -3.316
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -0.853
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -0.095
## alcohol 3.029
## prs_scaled:birth.x -2.762
## prs_scaled:HRT.ever1 -0.069
## prs_scaled:birth.y -0.498
## prs_scaled:factor(oc.cate3)1 -1.405
## prs_scaled:factor(oc.cate3)2 -1.099
## prs_scaled:factor(oc.cate3)3 -2.082
## prs_scaled:factor(oc.cate3)4 -2.729
## prs_scaled:age.menopause.scale -0.079
## prs_scaled:age.menarche.scale -0.437
## prs_scaled:BMI.scale -0.419
## prs_scaled:agegroups[50,60) -0.301
## prs_scaled:agegroups[60,70) -0.364
## prs_scaled:agegroups[70,80) -1.634
## prs_scaled:alcohol -1.534
## prs_scaled:height.scale -0.820
## prs_scaled:n.children.scale 0.121
## prs_scaled:age.firstbirth.group[25,35) 1.996
## prs_scaled:age.firstbirth.group[35,80) -0.739
## prs_scaled:age.firstbirth.group[80,1e+03) -0.280
## Pr(>|z|)
## (Intercept) < 2e-16
## prs_scaled 0.001058
## PC1 0.767491
## PC2 0.102821
## PC3 0.767559
## PC4 0.695238
## PC5 0.582192
## PC6 0.142232
## PC7 0.495073
## PC8 0.250934
## PC9 0.200812
## PC10 0.950390
## HRT.ever1 0.009835
## agegroups[50,60) 0.025146
## agegroups[60,70) 0.000735
## agegroups[70,80) 0.013696
## n.children.scale 0.050984
## birth.x 0.350580
## birth.y 0.713003
## age.firstbirth.group[25,35) 0.837352
## age.firstbirth.group[35,80) 0.028780
## age.firstbirth.group[80,1e+03) 0.982314
## height.scale 1.35e-07
## age.menarche.scale 0.513447
## age.menopause.scale 0.000222
## factor(oc.cate3)1 0.646105
## factor(oc.cate3)2 0.637441
## factor(oc.cate3)3 0.422178
## factor(oc.cate3)4 0.556217
## BMI.scale 6.10e-10
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.949472
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.486174
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 0.050577
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.213434
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.233180
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 0.383309
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.413727
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 0.176852
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.053029
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.002988
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 0.025479
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 0.170675
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 0.008768
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 3.46e-05
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 0.145629
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 0.006662
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 5.59e-05
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 0.001592
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 0.000912
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 0.393606
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 0.924067
## alcohol 0.002450
## prs_scaled:birth.x 0.005742
## prs_scaled:HRT.ever1 0.945215
## prs_scaled:birth.y 0.618723
## prs_scaled:factor(oc.cate3)1 0.160073
## prs_scaled:factor(oc.cate3)2 0.271796
## prs_scaled:factor(oc.cate3)3 0.037319
## prs_scaled:factor(oc.cate3)4 0.006349
## prs_scaled:age.menopause.scale 0.937288
## prs_scaled:age.menarche.scale 0.662055
## prs_scaled:BMI.scale 0.675564
## prs_scaled:agegroups[50,60) 0.763566
## prs_scaled:agegroups[60,70) 0.715648
## prs_scaled:agegroups[70,80) 0.102329
## prs_scaled:alcohol 0.124958
## prs_scaled:height.scale 0.412161
## prs_scaled:n.children.scale 0.903877
## prs_scaled:age.firstbirth.group[25,35) 0.045942
## prs_scaled:age.firstbirth.group[35,80) 0.460062
## prs_scaled:age.firstbirth.group[80,1e+03) 0.779512
##
## (Intercept) ***
## prs_scaled **
## PC1
## PC2
## PC3
## PC4
## PC5
## PC6
## PC7
## PC8
## PC9
## PC10
## HRT.ever1 **
## agegroups[50,60) *
## agegroups[60,70) ***
## agegroups[70,80) *
## n.children.scale .
## birth.x
## birth.y
## age.firstbirth.group[25,35)
## age.firstbirth.group[35,80) *
## age.firstbirth.group[80,1e+03)
## height.scale ***
## age.menarche.scale
## age.menopause.scale ***
## factor(oc.cate3)1
## factor(oc.cate3)2
## factor(oc.cate3)3
## factor(oc.cate3)4
## BMI.scale ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 .
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 .
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 *
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 **
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 ***
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023
## alcohol **
## prs_scaled:birth.x **
## prs_scaled:HRT.ever1
## prs_scaled:birth.y
## prs_scaled:factor(oc.cate3)1
## prs_scaled:factor(oc.cate3)2
## prs_scaled:factor(oc.cate3)3 *
## prs_scaled:factor(oc.cate3)4 **
## prs_scaled:age.menopause.scale
## prs_scaled:age.menarche.scale
## prs_scaled:BMI.scale
## prs_scaled:agegroups[50,60)
## prs_scaled:agegroups[60,70)
## prs_scaled:agegroups[70,80)
## prs_scaled:alcohol
## prs_scaled:height.scale
## prs_scaled:n.children.scale
## prs_scaled:age.firstbirth.group[25,35) *
## prs_scaled:age.firstbirth.group[35,80)
## prs_scaled:age.firstbirth.group[80,1e+03)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 19420 on 91264 degrees of freedom
## Residual deviance: 18767 on 91194 degrees of freedom
## AIC: 18909
##
## Number of Fisher Scoring iterations: 14
#Now let's select the control samples for the case/control study
table(dat_test_complete$breast_cancer)
##
## 0 1
## 89241 2024
#select 2024 controls who did not have breast cancer
control=dat_test_complete[which(dat_test_complete$breast_cancer==0),]
set.seed(10252022)
control=control[sample(1:dim(control)[1],size=2024,replace = F),]
dat_test_casecontrol=rbind(control,dat_test_complete[which(dat_test_complete$breast_cancer==1),])
dat_test_casecontrol$prs_scaled=scale(dat_test_casecontrol$prs_bc,center = T,scale = T)
dat_test_casecontrol$age.menarche.scale=scale(dat_test_casecontrol$age.menarche,center = T,scale=T)
dat_test_casecontrol$age.menopause.scale=scale(dat_test_casecontrol$age.menopause,center = T,scale=T)
dat_test_casecontrol$n.children.scale=scale(dat_test_casecontrol$n.children.win,center=T,scale = T)
dat_test_casecontrol$height.scale=scale(dat_test_casecontrol$height,center=T,scale = T)
dat_test_casecontrol$BMI.scale=scale(dat_test_casecontrol$BMI,center=T,scale = T)
dat_test_casecontrol$length.oc.scale=scale(dat_test_casecontrol$length.oc,center=T,scale = T)
dat_test_casecontrol$birth.x=scale(dat_test_casecontrol$birth.x,center=T,scale=T)
dat_test_casecontrol$birth.y=scale(dat_test_casecontrol$birth.y,center=T,scale=T)
dat_test_casecontrol.coordinate=dat_test_casecontrol[complete.cases(dat_test_casecontrol),]
table(dat_test_casecontrol.coordinate$breast_cancer)
##
## 0 1
## 2024 2024
dat_test_casecontrol.coordinate$assessment_center=factor(dat_test_casecontrol.coordinate$assessment_center)
dat_test_casecontrol.coordinate$assessment_center=relevel(dat_test_casecontrol.coordinate$assessment_center,ref = "11001")
fit_normal.coordinate1<-prs_e_function_gr(data=dat_test_casecontrol.coordinate,
formula = breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+length.oc.scale+BMI.scale+assessment_center+alcohol+prs_scaled:HRT.ever+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:length.oc.scale+prs_scaled:age.menopause.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group,
formula_prs = prs_scaled ~ PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+birth.x+birth.y,
numDeriv = F,
facVar="assessment_center")
## After removing missing values, the number of observations is 4048
## initial value 8390.902284
## iter 50 value 8369.798706
## iter 100 value 8368.161818
## iter 100 value 8368.161773
## iter 100 value 8368.161770
## final value 8368.161770
## converged
fit_normal.coordinate2<-prs_e_function_gr(data=dat_test_casecontrol.coordinate,
formula = breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+factor(oc.cate2)+BMI.scale+assessment_center+alcohol+prs_scaled:HRT.ever+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:factor(oc.cate2)+prs_scaled:age.menopause.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group,
formula_prs = prs_scaled ~ PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+birth.x+birth.y,
numDeriv = F,
facVar="assessment_center")
## After removing missing values, the number of observations is 4048
## initial value 8388.862534
## iter 50 value 8367.676436
## final value 8366.343437
## converged
fit_normal.coordinate3<-prs_e_function_gr(data=dat_test_casecontrol.coordinate,
formula = breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+factor(oc.cate3)+BMI.scale+assessment_center+alcohol+prs_scaled:HRT.ever+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:factor(oc.cate3)+prs_scaled:age.menopause.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group,
formula_prs = prs_scaled ~ PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+birth.x+birth.y,
numDeriv = F,
facVar="assessment_center")
## After removing missing values, the number of observations is 4048
## initial value 8391.674153
## iter 50 value 8366.035996
## iter 100 value 8364.536027
## final value 8364.535193
## converged
#Print the results, our method
fit_normal.coordinate1$res_normal
## Estimate Std.Error
## (Intercept) 3.948664e-02 3.422669e-01
## prs_scaled 5.567272e-01 1.962090e-01
## PC1 -2.260605e-03 9.282367e-03
## PC2 -9.034258e-03 1.116144e-02
## PC3 -2.504868e-03 1.683675e-02
## PC4 2.426211e-03 8.993225e-03
## PC5 -2.248847e-03 5.621667e-03
## PC6 -4.131319e-02 1.602939e-02
## PC7 -5.026927e-03 1.065833e-02
## PC8 2.027277e-02 1.237372e-02
## PC9 -3.664627e-03 8.243453e-03
## PC10 -1.795839e-02 1.577233e-02
## HRT.ever1 1.097781e-01 6.745237e-02
## agegroups[50,60) 3.813120e-01 2.378596e-01
## agegroups[60,70) 5.273348e-01 2.384501e-01
## agegroups[70,80) 4.843595e-01 4.800389e-01
## n.children.scale -7.691003e-02 5.179446e-02
## birth.x 2.096387e-02 4.607019e-02
## birth.y 1.141679e-02 5.450359e-02
## age.firstbirth.group[25,35) 1.559022e-02 7.746185e-02
## age.firstbirth.group[35,80) 2.778220e-01 1.687056e-01
## age.firstbirth.group[80,1e+03) -1.614229e-01 1.483240e-01
## height.scale 8.730861e-02 3.381184e-02
## age.menarche.scale 1.831520e-02 3.310839e-02
## age.menopause.scale 9.486220e-02 3.373300e-02
## length.oc.scale -7.725375e-03 3.370364e-02
## BMI.scale 1.375522e-01 3.365540e-02
## assessment_center10003 -9.858323e-01 9.552895e-01
## assessment_center11002 -7.939277e-01 2.712663e-01
## assessment_center11003 -5.697407e-01 2.837481e-01
## assessment_center11004 -6.346776e-01 2.754790e-01
## assessment_center11005 -5.498312e-01 2.767912e-01
## assessment_center11006 -6.721534e-01 2.633832e-01
## assessment_center11007 -4.991430e-01 2.487615e-01
## assessment_center11008 -6.516487e-01 2.469267e-01
## assessment_center11009 -5.839815e-01 2.487204e-01
## assessment_center11010 -8.304449e-01 2.397990e-01
## assessment_center11011 -6.872853e-01 2.421198e-01
## assessment_center11012 -8.493216e-01 3.063264e-01
## assessment_center11013 -7.760932e-01 2.468453e-01
## assessment_center11014 -1.031056e+00 2.537289e-01
## assessment_center11016 -7.207543e-01 2.414505e-01
## assessment_center11017 -8.759684e-01 2.695332e-01
## assessment_center11018 -1.140084e+00 2.714138e-01
## assessment_center11020 -1.039008e+00 2.639268e-01
## assessment_center11021 -9.233514e-01 2.634024e-01
## assessment_center11022 -7.682391e-01 5.010388e-01
## assessment_center11023 -1.387961e+01 4.300565e+02
## alcohol 2.351016e-01 8.038411e-02
## prs_scaled:HRT.ever1 -2.325342e-02 4.737374e-02
## prs_scaled:birth.x -7.854187e-02 3.721116e-02
## prs_scaled:birth.y -1.915056e-02 3.777037e-02
## prs_scaled:length.oc.scale -5.014684e-02 2.401896e-02
## prs_scaled:age.menopause.scale 2.002935e-05 2.399891e-02
## prs_scaled:age.menarche.scale -1.359233e-02 2.340060e-02
## prs_scaled:BMI.scale -1.177562e-02 2.303585e-02
## prs_scaled:agegroups[50,60) -2.190439e-02 1.877971e-01
## prs_scaled:agegroups[60,70) -3.747816e-02 1.878514e-01
## prs_scaled:agegroups[70,80) -5.474055e-01 3.473865e-01
## prs_scaled:alcohol -9.894633e-02 5.766611e-02
## prs_scaled:height.scale -1.265516e-02 2.366219e-02
## prs_scaled:n.children.scale 1.130654e-02 3.668144e-02
## prs_scaled:age.firstbirth.group[25,35) 8.385054e-02 5.439041e-02
## prs_scaled:age.firstbirth.group[35,80) -1.400071e-01 1.138158e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -3.353563e-02 1.050644e-01
## eta_(Intercept) -2.823509e-01 5.256166e-02
## eta_PC1 -6.243737e-03 4.185849e-03
## eta_PC2 -1.402430e-03 5.060852e-03
## eta_PC3 -2.661478e-03 7.773258e-03
## eta_PC4 -9.829818e-03 4.156795e-03
## eta_PC5 -9.089082e-04 2.515611e-03
## eta_PC6 2.558639e-03 6.559343e-03
## eta_PC7 1.940953e-03 5.040109e-03
## eta_PC8 1.641648e-03 5.496468e-03
## eta_PC9 4.412288e-03 3.631581e-03
## eta_PC10 4.939431e-03 7.068537e-03
## eta_birth.x -1.895135e-03 2.582357e-02
## eta_birth.y -1.434456e-03 2.706437e-02
## sigma_stratadata[, facVar]11001 9.089072e-01 5.722480e-02
## sigma_stratadata[, facVar]10003 3.818508e-01 1.290926e-01
## sigma_stratadata[, facVar]11002 8.986934e-01 4.861801e-02
## sigma_stratadata[, facVar]11003 9.661814e-01 5.099034e-02
## sigma_stratadata[, facVar]11004 9.392241e-01 4.437291e-02
## sigma_stratadata[, facVar]11005 9.602117e-01 4.831127e-02
## sigma_stratadata[, facVar]11006 9.519442e-01 4.738247e-02
## sigma_stratadata[, facVar]11007 9.692230e-01 3.789705e-02
## sigma_stratadata[, facVar]11008 9.995270e-01 4.021558e-02
## sigma_stratadata[, facVar]11009 9.858991e-01 3.703801e-02
## sigma_stratadata[, facVar]11010 9.385364e-01 3.360697e-02
## sigma_stratadata[, facVar]11011 9.444339e-01 3.306721e-02
## sigma_stratadata[, facVar]11012 9.276127e-01 6.564758e-02
## sigma_stratadata[, facVar]11013 1.027898e+00 4.075617e-02
## sigma_stratadata[, facVar]11014 9.866691e-01 4.367755e-02
## sigma_stratadata[, facVar]11016 9.947623e-01 3.580687e-02
## sigma_stratadata[, facVar]11017 9.841431e-01 5.021236e-02
## sigma_stratadata[, facVar]11018 9.981146e-01 5.219447e-02
## sigma_stratadata[, facVar]11020 9.687747e-01 4.689130e-02
## sigma_stratadata[, facVar]11021 1.009229e+00 5.011865e-02
## sigma_stratadata[, facVar]11022 1.160742e+00 1.501061e-01
## sigma_stratadata[, facVar]11023 5.669919e-01 2.023234e-01
## Z.value Pvalue
## (Intercept) 0.115367976 9.081535e-01
## prs_scaled 2.837419428 4.547982e-03
## PC1 -0.243537579 8.075890e-01
## PC2 -0.809416604 4.182756e-01
## PC3 -0.148773860 8.817321e-01
## PC4 0.269782043 7.873279e-01
## PC5 -0.400032004 6.891329e-01
## PC6 -2.577340549 9.956381e-03
## PC7 -0.471643009 6.371816e-01
## PC8 1.638373164 1.013439e-01
## PC9 -0.444549980 6.566450e-01
## PC10 -1.138600747 2.548697e-01
## HRT.ever1 1.627491044 1.036328e-01
## agegroups[50,60) 1.603097169 1.089132e-01
## agegroups[60,70) 2.211509898 2.700055e-02
## agegroups[70,80) 1.009000521 3.129744e-01
## n.children.scale -1.484908464 1.375681e-01
## birth.x 0.455041991 6.490790e-01
## birth.y 0.209468660 8.340824e-01
## age.firstbirth.group[25,35) 0.201263197 8.404928e-01
## age.firstbirth.group[35,80) 1.646786553 9.960193e-02
## age.firstbirth.group[80,1e+03) -1.088312788 2.764570e-01
## height.scale 2.582190084 9.817549e-03
## age.menarche.scale 0.553189102 5.801339e-01
## age.menopause.scale 2.812148392 4.921179e-03
## length.oc.scale -0.229214842 8.187019e-01
## BMI.scale 4.087075928 4.368442e-05
## assessment_center10003 -1.031972249 3.020851e-01
## assessment_center11002 -2.926746058 3.425284e-03
## assessment_center11003 -2.007910290 4.465283e-02
## assessment_center11004 -2.303905515 2.122795e-02
## assessment_center11005 -1.986447363 4.698367e-02
## assessment_center11006 -2.551998013 1.071071e-02
## assessment_center11007 -2.006512179 4.480163e-02
## assessment_center11008 -2.639037445 8.314180e-03
## assessment_center11009 -2.347943713 1.887737e-02
## assessment_center11010 -3.463087438 5.340148e-04
## assessment_center11011 -2.838617280 4.530947e-03
## assessment_center11012 -2.772603681 5.560980e-03
## assessment_center11013 -3.144047016 1.666287e-03
## assessment_center11014 -4.063611538 4.831922e-05
## assessment_center11016 -2.985101854 2.834839e-03
## assessment_center11017 -3.249946503 1.154267e-03
## assessment_center11018 -4.200536660 2.662830e-05
## assessment_center11020 -3.936726725 8.260058e-05
## assessment_center11021 -3.505478837 4.557867e-04
## assessment_center11022 -1.533292567 1.252038e-01
## assessment_center11023 -0.032273918 9.742536e-01
## alcohol 2.924727934 3.447575e-03
## prs_scaled:HRT.ever1 -0.490850468 6.235322e-01
## prs_scaled:birth.x -2.110707141 3.479749e-02
## prs_scaled:birth.y -0.507025991 6.121366e-01
## prs_scaled:length.oc.scale -2.087802149 3.681569e-02
## prs_scaled:age.menopause.scale 0.000834594 9.993341e-01
## prs_scaled:age.menarche.scale -0.580853788 5.613390e-01
## prs_scaled:BMI.scale -0.511186638 6.092204e-01
## prs_scaled:agegroups[50,60) -0.116638603 9.071464e-01
## prs_scaled:agegroups[60,70) -0.199509591 8.418641e-01
## prs_scaled:agegroups[70,80) -1.575782381 1.150760e-01
## prs_scaled:alcohol -1.715848802 8.618972e-02
## prs_scaled:height.scale -0.534826380 5.927699e-01
## prs_scaled:n.children.scale 0.308236024 7.579027e-01
## prs_scaled:age.firstbirth.group[25,35) 1.541641862 1.231606e-01
## prs_scaled:age.firstbirth.group[35,80) -1.230119774 2.186523e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -0.319191207 7.495815e-01
## eta_(Intercept) -5.371802382 7.795351e-08
## eta_PC1 -1.491629764 1.357962e-01
## eta_PC2 -0.277113501 7.816930e-01
## eta_PC3 -0.342388961 7.320582e-01
## eta_PC4 -2.364759039 1.804181e-02
## eta_PC5 -0.361307129 7.178699e-01
## eta_PC6 0.390075591 6.964807e-01
## eta_PC7 0.385101335 7.001623e-01
## eta_PC8 0.298673301 7.651893e-01
## eta_PC9 1.214977204 2.243748e-01
## eta_PC10 0.698791168 4.846825e-01
## eta_birth.x -0.073387805 9.414975e-01
## eta_birth.y -0.053001646 9.577306e-01
## sigma_stratadata[, facVar]11001 15.883098482 8.297625e-57
## sigma_stratadata[, facVar]10003 2.957960652 3.096817e-03
## sigma_stratadata[, facVar]11002 18.484784332 2.737914e-76
## sigma_stratadata[, facVar]11003 18.948321814 4.558916e-80
## sigma_stratadata[, facVar]11004 21.166609570 1.940233e-99
## sigma_stratadata[, facVar]11005 19.875519308 6.629693e-88
## sigma_stratadata[, facVar]11006 20.090639984 8.910614e-90
## sigma_stratadata[, facVar]11007 25.575155321 2.883581e-144
## sigma_stratadata[, facVar]11008 24.854223902 2.327788e-136
## sigma_stratadata[, facVar]11009 26.618578290 4.137585e-156
## sigma_stratadata[, facVar]11010 27.926839933 1.260110e-171
## sigma_stratadata[, facVar]11011 28.561037858 2.048756e-179
## sigma_stratadata[, facVar]11012 14.130188579 2.474807e-45
## sigma_stratadata[, facVar]11013 25.220666562 2.377099e-140
## sigma_stratadata[, facVar]11014 22.589845189 5.453844e-113
## sigma_stratadata[, facVar]11016 27.781325603 7.293567e-170
## sigma_stratadata[, facVar]11017 19.599619447 1.557845e-85
## sigma_stratadata[, facVar]11018 19.122996512 1.624980e-81
## sigma_stratadata[, facVar]11020 20.660009250 7.934912e-95
## sigma_stratadata[, facVar]11021 20.136791113 3.513769e-90
## sigma_stratadata[, facVar]11022 7.732806973 1.052007e-14
## sigma_stratadata[, facVar]11023 2.802404178 5.072328e-03
fit_normal.coordinate2$res_normal
## Estimate Std.Error
## (Intercept) 1.143833e-01 3.496256e-01
## prs_scaled 6.319211e-01 2.020940e-01
## PC1 -2.070278e-03 9.272338e-03
## PC2 -9.256453e-03 1.116082e-02
## PC3 -2.482732e-03 1.684083e-02
## PC4 2.789588e-03 8.995437e-03
## PC5 -2.545690e-03 5.625386e-03
## PC6 -4.190635e-02 1.605306e-02
## PC7 -5.524403e-03 1.066883e-02
## PC8 1.964101e-02 1.239240e-02
## PC9 -4.084408e-03 8.249830e-03
## PC10 -1.856019e-02 1.578256e-02
## HRT.ever1 1.138537e-01 6.766522e-02
## agegroups[50,60) 3.847854e-01 2.379479e-01
## agegroups[60,70) 5.187767e-01 2.384781e-01
## agegroups[70,80) 4.655907e-01 4.805113e-01
## n.children.scale -7.449453e-02 5.177401e-02
## birth.x 2.020331e-02 4.606847e-02
## birth.y 1.241593e-02 5.451456e-02
## age.firstbirth.group[25,35) 1.723651e-02 7.749110e-02
## age.firstbirth.group[35,80) 2.795794e-01 1.687465e-01
## age.firstbirth.group[80,1e+03) -1.722964e-01 1.486196e-01
## height.scale 8.787780e-02 3.383175e-02
## age.menarche.scale 1.794572e-02 3.311777e-02
## age.menopause.scale 9.542472e-02 3.375995e-02
## factor(oc.cate2)1 -1.181491e-01 8.746166e-02
## factor(oc.cate2)2 -5.718852e-02 9.221518e-02
## BMI.scale 1.380113e-01 3.367526e-02
## assessment_center10003 -9.940654e-01 9.550528e-01
## assessment_center11002 -7.966172e-01 2.712466e-01
## assessment_center11003 -5.727424e-01 2.837607e-01
## assessment_center11004 -6.428171e-01 2.755457e-01
## assessment_center11005 -5.517754e-01 2.767953e-01
## assessment_center11006 -6.791771e-01 2.634324e-01
## assessment_center11007 -4.997692e-01 2.487943e-01
## assessment_center11008 -6.571765e-01 2.469160e-01
## assessment_center11009 -5.780287e-01 2.487112e-01
## assessment_center11010 -8.354209e-01 2.397895e-01
## assessment_center11011 -6.907660e-01 2.420599e-01
## assessment_center11012 -8.486605e-01 3.063364e-01
## assessment_center11013 -7.777573e-01 2.467860e-01
## assessment_center11014 -1.029529e+00 2.536799e-01
## assessment_center11016 -7.260955e-01 2.414270e-01
## assessment_center11017 -8.837694e-01 2.695998e-01
## assessment_center11018 -1.144572e+00 2.712972e-01
## assessment_center11020 -1.042954e+00 2.638730e-01
## assessment_center11021 -9.296488e-01 2.633687e-01
## assessment_center11022 -7.927843e-01 5.014704e-01
## assessment_center11023 -1.390991e+01 4.342067e+02
## alcohol 2.399167e-01 8.049237e-02
## prs_scaled:HRT.ever1 -1.938411e-02 4.750312e-02
## prs_scaled:birth.x -7.862657e-02 3.721077e-02
## prs_scaled:birth.y -1.837563e-02 3.775392e-02
## prs_scaled:factor(oc.cate2)1 -5.725996e-02 6.057236e-02
## prs_scaled:factor(oc.cate2)2 -1.486511e-01 6.418316e-02
## prs_scaled:age.menopause.scale -2.021497e-03 2.402176e-02
## prs_scaled:age.menarche.scale -1.353702e-02 2.340212e-02
## prs_scaled:BMI.scale -1.200163e-02 2.302626e-02
## prs_scaled:agegroups[50,60) -2.102673e-02 1.879070e-01
## prs_scaled:agegroups[60,70) -4.023784e-02 1.879376e-01
## prs_scaled:agegroups[70,80) -5.510212e-01 3.472439e-01
## prs_scaled:alcohol -9.743896e-02 5.773019e-02
## prs_scaled:height.scale -1.127736e-02 2.368171e-02
## prs_scaled:n.children.scale 1.277305e-02 3.665719e-02
## prs_scaled:age.firstbirth.group[25,35) 8.250360e-02 5.439157e-02
## prs_scaled:age.firstbirth.group[35,80) -1.345102e-01 1.138379e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -3.648980e-02 1.052210e-01
## eta_(Intercept) -2.828490e-01 5.256334e-02
## eta_PC1 -6.310626e-03 4.186107e-03
## eta_PC2 -1.457553e-03 5.060929e-03
## eta_PC3 -2.590204e-03 7.772518e-03
## eta_PC4 -9.794635e-03 4.157308e-03
## eta_PC5 -9.134795e-04 2.515632e-03
## eta_PC6 2.458747e-03 6.562283e-03
## eta_PC7 1.933820e-03 5.040290e-03
## eta_PC8 1.584608e-03 5.498501e-03
## eta_PC9 4.370385e-03 3.632141e-03
## eta_PC10 4.829798e-03 7.069596e-03
## eta_birth.x -1.824304e-03 2.580971e-02
## eta_birth.y -1.416815e-03 2.704950e-02
## sigma_stratadata[, facVar]11001 9.082338e-01 5.711694e-02
## sigma_stratadata[, facVar]10003 3.828844e-01 1.303017e-01
## sigma_stratadata[, facVar]11002 8.985844e-01 4.859521e-02
## sigma_stratadata[, facVar]11003 9.667816e-01 5.106369e-02
## sigma_stratadata[, facVar]11004 9.385829e-01 4.429839e-02
## sigma_stratadata[, facVar]11005 9.600718e-01 4.828930e-02
## sigma_stratadata[, facVar]11006 9.514111e-01 4.730712e-02
## sigma_stratadata[, facVar]11007 9.699872e-01 3.797949e-02
## sigma_stratadata[, facVar]11008 9.985094e-01 4.011958e-02
## sigma_stratadata[, facVar]11009 9.861407e-01 3.706165e-02
## sigma_stratadata[, facVar]11010 9.383851e-01 3.359246e-02
## sigma_stratadata[, facVar]11011 9.446947e-01 3.308987e-02
## sigma_stratadata[, facVar]11012 9.278460e-01 6.569226e-02
## sigma_stratadata[, facVar]11013 1.027825e+00 4.075064e-02
## sigma_stratadata[, facVar]11014 9.861788e-01 4.361588e-02
## sigma_stratadata[, facVar]11016 9.947505e-01 3.580433e-02
## sigma_stratadata[, facVar]11017 9.843239e-01 5.024189e-02
## sigma_stratadata[, facVar]11018 9.975388e-01 5.211610e-02
## sigma_stratadata[, facVar]11020 9.686957e-01 4.687530e-02
## sigma_stratadata[, facVar]11021 1.008143e+00 4.997772e-02
## sigma_stratadata[, facVar]11022 1.157042e+00 1.489144e-01
## sigma_stratadata[, facVar]11023 5.661837e-01 2.016666e-01
## Z.value Pvalue
## (Intercept) 0.32715928 7.435474e-01
## prs_scaled 3.12686717 1.766797e-03
## PC1 -0.22327465 8.233218e-01
## PC2 -0.82937035 4.068949e-01
## PC3 -0.14742336 8.827979e-01
## PC4 0.31011142 7.564762e-01
## PC5 -0.45253603 6.508829e-01
## PC6 -2.61049013 9.041258e-03
## PC7 -0.51780753 6.045926e-01
## PC8 1.58492391 1.129836e-01
## PC9 -0.49508994 6.205366e-01
## PC10 -1.17599384 2.395973e-01
## HRT.ever1 1.68260318 9.245194e-02
## agegroups[50,60) 1.61709900 1.058569e-01
## agegroups[60,70) 2.17536372 2.960287e-02
## agegroups[70,80) 0.96894837 3.325709e-01
## n.children.scale -1.43884029 1.501958e-01
## birth.x 0.43854972 6.609878e-01
## birth.y 0.22775444 8.198371e-01
## age.firstbirth.group[25,35) 0.22243217 8.239775e-01
## age.firstbirth.group[35,80) 1.65680081 9.755975e-02
## age.firstbirth.group[80,1e+03) -1.15931105 2.463294e-01
## height.scale 2.59749543 9.390637e-03
## age.menarche.scale 0.54187600 5.879039e-01
## age.menopause.scale 2.82656548 4.705012e-03
## factor(oc.cate2)1 -1.35086719 1.767380e-01
## factor(oc.cate2)2 -0.62016379 5.351500e-01
## BMI.scale 4.09830020 4.161953e-05
## assessment_center10003 -1.04084865 2.979458e-01
## assessment_center11002 -2.93687411 3.315387e-03
## assessment_center11003 -2.01839936 4.354969e-02
## assessment_center11004 -2.33288764 1.965404e-02
## assessment_center11005 -1.99344185 4.621309e-02
## assessment_center11006 -2.57818394 9.932111e-03
## assessment_center11007 -2.00876443 4.456212e-02
## assessment_center11008 -2.66153903 7.778432e-03
## assessment_center11009 -2.32409598 2.012035e-02
## assessment_center11010 -3.48397547 4.940248e-04
## assessment_center11011 -2.85369847 4.321353e-03
## assessment_center11012 -2.77035453 5.599531e-03
## assessment_center11013 -3.15154536 1.624089e-03
## assessment_center11014 -4.05837667 4.941502e-05
## assessment_center11016 -3.00751526 2.633929e-03
## assessment_center11017 -3.27807867 1.045163e-03
## assessment_center11018 -4.21888491 2.455136e-05
## assessment_center11020 -3.95248395 7.734412e-05
## assessment_center11021 -3.52983737 4.158152e-04
## assessment_center11022 -1.58091951 1.138964e-01
## assessment_center11023 -0.03203522 9.744440e-01
## alcohol 2.98061443 2.876707e-03
## prs_scaled:HRT.ever1 -0.40805968 6.832299e-01
## prs_scaled:birth.x -2.11300566 3.460028e-02
## prs_scaled:birth.y -0.48672113 6.264560e-01
## prs_scaled:factor(oc.cate2)1 -0.94531505 3.444981e-01
## prs_scaled:factor(oc.cate2)2 -2.31604539 2.055579e-02
## prs_scaled:age.menopause.scale -0.08415275 9.329350e-01
## prs_scaled:age.menarche.scale -0.57845257 5.629586e-01
## prs_scaled:BMI.scale -0.52121500 6.022170e-01
## prs_scaled:agegroups[50,60) -0.11189967 9.109030e-01
## prs_scaled:agegroups[60,70) -0.21410215 8.304674e-01
## prs_scaled:agegroups[70,80) -1.58684204 1.125484e-01
## prs_scaled:alcohol -1.68783375 9.144315e-02
## prs_scaled:height.scale -0.47620539 6.339281e-01
## prs_scaled:n.children.scale 0.34844594 7.275053e-01
## prs_scaled:age.firstbirth.group[25,35) 1.51684545 1.293057e-01
## prs_scaled:age.firstbirth.group[35,80) -1.18159398 2.373668e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -0.34679204 7.287476e-01
## eta_(Intercept) -5.38110828 7.402865e-08
## eta_PC1 -1.50751663 1.316783e-01
## eta_PC2 -0.28800097 7.733460e-01
## eta_PC3 -0.33325157 7.389444e-01
## eta_PC4 -2.35600437 1.847270e-02
## eta_PC5 -0.36312134 7.165142e-01
## eta_PC6 0.37467864 7.078995e-01
## eta_PC7 0.38367247 7.012212e-01
## eta_PC8 0.28818903 7.732020e-01
## eta_PC9 1.20325305 2.288784e-01
## eta_PC10 0.68317880 4.944939e-01
## eta_birth.x -0.07068284 9.436502e-01
## eta_birth.y -0.05237860 9.582270e-01
## sigma_stratadata[, facVar]11001 15.90130234 6.206104e-57
## sigma_stratadata[, facVar]10003 2.93844569 3.298624e-03
## sigma_stratadata[, facVar]11002 18.49121492 2.430171e-76
## sigma_stratadata[, facVar]11003 18.93285910 6.115152e-80
## sigma_stratadata[, facVar]11004 21.18774161 1.238991e-99
## sigma_stratadata[, facVar]11005 19.88166950 5.864948e-88
## sigma_stratadata[, facVar]11006 20.11137366 5.867619e-90
## sigma_stratadata[, facVar]11007 25.53976632 7.133959e-144
## sigma_stratadata[, facVar]11008 24.88833351 9.952133e-137
## sigma_stratadata[, facVar]11009 26.60811301 5.468589e-156
## sigma_stratadata[, facVar]11010 27.93439302 1.020167e-171
## sigma_stratadata[, facVar]11011 28.54936271 2.860587e-179
## sigma_stratadata[, facVar]11012 14.12412954 2.697119e-45
## sigma_stratadata[, facVar]11013 25.22230940 2.280469e-140
## sigma_stratadata[, facVar]11014 22.61054456 3.413023e-113
## sigma_stratadata[, facVar]11016 27.78296202 6.968994e-170
## sigma_stratadata[, facVar]11017 19.59169601 1.820245e-85
## sigma_stratadata[, facVar]11018 19.14070083 1.157033e-81
## sigma_stratadata[, facVar]11020 20.66537687 7.100066e-95
## sigma_stratadata[, facVar]11021 20.17185553 1.730237e-90
## sigma_stratadata[, facVar]11022 7.76984462 7.858246e-15
## sigma_stratadata[, facVar]11023 2.80752323 4.992408e-03
fit_normal.coordinate3$res_normal
## Estimate Std.Error
## (Intercept) 1.322011e-01 3.499958e-01
## prs_scaled 6.367533e-01 2.021180e-01
## PC1 -1.850946e-03 9.271079e-03
## PC2 -9.398864e-03 1.117055e-02
## PC3 -1.970011e-03 1.685374e-02
## PC4 2.770548e-03 8.999440e-03
## PC5 -2.637584e-03 5.628723e-03
## PC6 -4.185826e-02 1.610184e-02
## PC7 -5.094107e-03 1.067844e-02
## PC8 1.945790e-02 1.241537e-02
## PC9 -4.175635e-03 8.256584e-03
## PC10 -1.887346e-02 1.579004e-02
## HRT.ever1 1.147030e-01 6.770202e-02
## agegroups[50,60) 3.722819e-01 2.382826e-01
## agegroups[60,70) 5.008160e-01 2.389267e-01
## agegroups[70,80) 4.439550e-01 4.808832e-01
## n.children.scale -7.565547e-02 5.183995e-02
## birth.x 2.183244e-02 4.611032e-02
## birth.y 1.063284e-02 5.453532e-02
## age.firstbirth.group[25,35) 1.572182e-02 7.753043e-02
## age.firstbirth.group[35,80) 2.742498e-01 1.688651e-01
## age.firstbirth.group[80,1e+03) -1.707966e-01 1.487208e-01
## height.scale 8.827477e-02 3.385064e-02
## age.menarche.scale 1.874234e-02 3.314140e-02
## age.menopause.scale 9.759685e-02 3.380240e-02
## factor(oc.cate3)1 -1.146778e-01 9.962546e-02
## factor(oc.cate3)2 -1.241402e-01 1.019382e-01
## factor(oc.cate3)3 4.261436e-02 1.097103e-01
## factor(oc.cate3)4 -1.441037e-01 1.055874e-01
## BMI.scale 1.382541e-01 3.369213e-02
## assessment_center10003 -1.021523e+00 9.564248e-01
## assessment_center11002 -7.964777e-01 2.714002e-01
## assessment_center11003 -5.757292e-01 2.841500e-01
## assessment_center11004 -6.428831e-01 2.756726e-01
## assessment_center11005 -5.515785e-01 2.769601e-01
## assessment_center11006 -6.803446e-01 2.635296e-01
## assessment_center11007 -5.086664e-01 2.489972e-01
## assessment_center11008 -6.536859e-01 2.470162e-01
## assessment_center11009 -5.780593e-01 2.488821e-01
## assessment_center11010 -8.393380e-01 2.399584e-01
## assessment_center11011 -6.884303e-01 2.422241e-01
## assessment_center11012 -8.585367e-01 3.065301e-01
## assessment_center11013 -7.758307e-01 2.469358e-01
## assessment_center11014 -1.025822e+00 2.537957e-01
## assessment_center11016 -7.264878e-01 2.415214e-01
## assessment_center11017 -8.934081e-01 2.697337e-01
## assessment_center11018 -1.135855e+00 2.714778e-01
## assessment_center11020 -1.047318e+00 2.639590e-01
## assessment_center11021 -9.237389e-01 2.634548e-01
## assessment_center11022 -7.849327e-01 5.017214e-01
## assessment_center11023 -1.393009e+01 4.396332e+02
## alcohol 2.444591e-01 8.058532e-02
## prs_scaled:HRT.ever1 -1.933169e-02 4.752234e-02
## prs_scaled:birth.x -7.808567e-02 3.722136e-02
## prs_scaled:birth.y -1.884832e-02 3.777626e-02
## prs_scaled:factor(oc.cate3)1 -6.663107e-02 6.943037e-02
## prs_scaled:factor(oc.cate3)2 -4.755356e-02 7.098707e-02
## prs_scaled:factor(oc.cate3)3 -1.221756e-01 7.569109e-02
## prs_scaled:factor(oc.cate3)4 -1.736876e-01 7.480506e-02
## prs_scaled:age.menopause.scale -1.445074e-03 2.403370e-02
## prs_scaled:age.menarche.scale -1.304529e-02 2.341047e-02
## prs_scaled:BMI.scale -1.179838e-02 2.303611e-02
## prs_scaled:agegroups[50,60) -2.609236e-02 1.879265e-01
## prs_scaled:agegroups[60,70) -4.510058e-02 1.880180e-01
## prs_scaled:agegroups[70,80) -5.585333e-01 3.473501e-01
## prs_scaled:alcohol -9.729574e-02 5.777404e-02
## prs_scaled:height.scale -1.111525e-02 2.368190e-02
## prs_scaled:n.children.scale 1.304029e-02 3.671553e-02
## prs_scaled:age.firstbirth.group[25,35) 8.214459e-02 5.440779e-02
## prs_scaled:age.firstbirth.group[35,80) -1.349295e-01 1.138737e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -3.484424e-02 1.052932e-01
## eta_(Intercept) -2.824238e-01 5.256379e-02
## eta_PC1 -6.289158e-03 4.185568e-03
## eta_PC2 -1.470220e-03 5.060148e-03
## eta_PC3 -2.482129e-03 7.773657e-03
## eta_PC4 -9.771823e-03 4.157577e-03
## eta_PC5 -9.243851e-04 2.515628e-03
## eta_PC6 2.473590e-03 6.561012e-03
## eta_PC7 1.982095e-03 5.040737e-03
## eta_PC8 1.565566e-03 5.498229e-03
## eta_PC9 4.372106e-03 3.631928e-03
## eta_PC10 4.831467e-03 7.069976e-03
## eta_birth.x -1.833114e-03 2.580439e-02
## eta_birth.y -1.380910e-03 2.704577e-02
## sigma_stratadata[, facVar]11001 9.081064e-01 5.710089e-02
## sigma_stratadata[, facVar]10003 3.843039e-01 1.312299e-01
## sigma_stratadata[, facVar]11002 8.983847e-01 4.856955e-02
## sigma_stratadata[, facVar]11003 9.671056e-01 5.111672e-02
## sigma_stratadata[, facVar]11004 9.384501e-01 4.428256e-02
## sigma_stratadata[, facVar]11005 9.597507e-01 4.824817e-02
## sigma_stratadata[, facVar]11006 9.512984e-01 4.729225e-02
## sigma_stratadata[, facVar]11007 9.694363e-01 3.793234e-02
## sigma_stratadata[, facVar]11008 9.985661e-01 4.012606e-02
## sigma_stratadata[, facVar]11009 9.861901e-01 3.707037e-02
## sigma_stratadata[, facVar]11010 9.382374e-01 3.357968e-02
## sigma_stratadata[, facVar]11011 9.446911e-01 3.308797e-02
## sigma_stratadata[, facVar]11012 9.276220e-01 6.564295e-02
## sigma_stratadata[, facVar]11013 1.027713e+00 4.073696e-02
## sigma_stratadata[, facVar]11014 9.862002e-01 4.362215e-02
## sigma_stratadata[, facVar]11016 9.946471e-01 3.579466e-02
## sigma_stratadata[, facVar]11017 9.838511e-01 5.018133e-02
## sigma_stratadata[, facVar]11018 9.977893e-01 5.215113e-02
## sigma_stratadata[, facVar]11020 9.683496e-01 4.683644e-02
## sigma_stratadata[, facVar]11021 1.008301e+00 5.000200e-02
## sigma_stratadata[, facVar]11022 1.156663e+00 1.487671e-01
## sigma_stratadata[, facVar]11023 5.656962e-01 2.012569e-01
## Z.value Pvalue
## (Intercept) 0.37772202 7.056371e-01
## prs_scaled 3.15040378 1.630450e-03
## PC1 -0.19964733 8.417564e-01
## PC2 -0.84139652 4.001258e-01
## PC3 -0.11688866 9.069483e-01
## PC4 0.30785783 7.581905e-01
## PC5 -0.46859363 6.393601e-01
## PC6 -2.59959524 9.333378e-03
## PC7 -0.47704596 6.333294e-01
## PC8 1.56724228 1.170581e-01
## PC9 -0.50573394 6.130434e-01
## PC10 -1.19527605 2.319792e-01
## HRT.ever1 1.69423320 9.022098e-02
## agegroups[50,60) 1.56235465 1.182045e-01
## agegroups[60,70) 2.09610693 3.607271e-02
## agegroups[70,80) 0.92320769 3.558990e-01
## n.children.scale -1.45940474 1.444537e-01
## birth.x 0.47348280 6.358688e-01
## birth.y 0.19497166 8.454151e-01
## age.firstbirth.group[25,35) 0.20278260 8.393050e-01
## age.firstbirth.group[35,80) 1.62407641 1.043595e-01
## age.firstbirth.group[80,1e+03) -1.14843804 2.507878e-01
## height.scale 2.60777269 9.113345e-03
## age.menarche.scale 0.56552662 5.717156e-01
## age.menopause.scale 2.88727597 3.885932e-03
## factor(oc.cate3)1 -1.15108964 2.496954e-01
## factor(oc.cate3)2 -1.21779772 2.233009e-01
## factor(oc.cate3)3 0.38842616 6.977007e-01
## factor(oc.cate3)4 -1.36478093 1.723219e-01
## BMI.scale 4.10345427 4.070269e-05
## assessment_center10003 -1.06806408 2.854916e-01
## assessment_center11002 -2.93469779 3.338727e-03
## assessment_center11003 -2.02614524 4.274990e-02
## assessment_center11004 -2.33205280 1.969791e-02
## assessment_center11005 -1.99154504 4.642100e-02
## assessment_center11006 -2.58166322 9.832548e-03
## assessment_center11007 -2.04285996 4.106630e-02
## assessment_center11008 -2.64632798 8.137088e-03
## assessment_center11009 -2.32262349 2.019939e-02
## assessment_center11010 -3.49784846 4.690276e-04
## assessment_center11011 -2.84212086 4.481450e-03
## assessment_center11012 -2.80082373 5.097235e-03
## assessment_center11013 -3.14183138 1.678947e-03
## assessment_center11014 -4.04192209 5.301485e-05
## assessment_center11016 -3.00796429 2.630040e-03
## assessment_center11017 -3.31218531 9.257021e-04
## assessment_center11018 -4.18397250 2.864588e-05
## assessment_center11020 -3.96773106 7.256015e-05
## assessment_center11021 -3.50625194 4.544648e-04
## assessment_center11022 -1.56447916 1.177051e-01
## assessment_center11023 -0.03168571 9.747227e-01
## alcohol 3.03354446 2.416991e-03
## prs_scaled:HRT.ever1 -0.40679173 6.841610e-01
## prs_scaled:birth.x -2.09787235 3.591642e-02
## prs_scaled:birth.y -0.49894625 6.178173e-01
## prs_scaled:factor(oc.cate3)1 -0.95968192 3.372153e-01
## prs_scaled:factor(oc.cate3)2 -0.66989049 5.029276e-01
## prs_scaled:factor(oc.cate3)3 -1.61413417 1.064983e-01
## prs_scaled:factor(oc.cate3)4 -2.32186938 2.023997e-02
## prs_scaled:age.menopause.scale -0.06012699 9.520545e-01
## prs_scaled:age.menarche.scale -0.55724195 5.773621e-01
## prs_scaled:BMI.scale -0.51216906 6.085327e-01
## prs_scaled:agegroups[50,60) -0.13884346 8.895739e-01
## prs_scaled:agegroups[60,70) -0.23987368 8.104282e-01
## prs_scaled:agegroups[70,80) -1.60798374 1.078387e-01
## prs_scaled:alcohol -1.68407354 9.216746e-02
## prs_scaled:height.scale -0.46935649 6.388148e-01
## prs_scaled:n.children.scale 0.35517104 7.224615e-01
## prs_scaled:age.firstbirth.group[25,35) 1.50979449 1.310959e-01
## prs_scaled:age.firstbirth.group[35,80) -1.18490449 2.360552e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -0.33092580 7.407005e-01
## eta_(Intercept) -5.37297174 7.744947e-08
## eta_PC1 -1.50258189 1.329469e-01
## eta_PC2 -0.29054886 7.713964e-01
## eta_PC3 -0.31930005 7.494990e-01
## eta_PC4 -2.35036495 1.875501e-02
## eta_PC5 -0.36745696 7.132782e-01
## eta_PC6 0.37701349 7.061636e-01
## eta_PC7 0.39321532 6.941605e-01
## eta_PC8 0.28474004 7.758433e-01
## eta_PC9 1.20379743 2.286679e-01
## eta_PC10 0.68337815 4.943679e-01
## eta_birth.x -0.07103884 9.433668e-01
## eta_birth.y -0.05105824 9.592791e-01
## sigma_stratadata[, facVar]11001 15.90354243 5.988079e-57
## sigma_stratadata[, facVar]10003 2.92847724 3.406268e-03
## sigma_stratadata[, facVar]11002 18.49687224 2.188094e-76
## sigma_stratadata[, facVar]11003 18.91955527 7.871588e-80
## sigma_stratadata[, facVar]11004 21.19231950 1.124206e-99
## sigma_stratadata[, facVar]11005 19.89196139 4.776967e-88
## sigma_stratadata[, facVar]11006 20.11531205 5.419697e-90
## sigma_stratadata[, facVar]11007 25.55698404 4.591972e-144
## sigma_stratadata[, facVar]11008 24.88572640 1.062038e-136
## sigma_stratadata[, facVar]11009 26.60318670 6.235588e-156
## sigma_stratadata[, facVar]11010 27.94063309 8.567682e-172
## sigma_stratadata[, facVar]11011 28.55089605 2.737914e-179
## sigma_stratadata[, facVar]11012 14.13132889 2.435054e-45
## sigma_stratadata[, facVar]11013 25.22802103 1.974033e-140
## sigma_stratadata[, facVar]11014 22.60778464 3.633221e-113
## sigma_stratadata[, facVar]11016 27.78758029 6.128715e-170
## sigma_stratadata[, facVar]11017 19.60592028 1.376398e-85
## sigma_stratadata[, facVar]11018 19.13265194 1.350272e-81
## sigma_stratadata[, facVar]11020 20.67513376 5.800574e-95
## sigma_stratadata[, facVar]11021 20.16522328 1.978518e-90
## sigma_stratadata[, facVar]11022 7.77499406 7.545095e-15
## sigma_stratadata[, facVar]11023 2.81081650 4.941596e-03
#Logistic regression on the case-control samples
fit_normal.coordinate1$res_glm
## Estimate Std. Error
## (Intercept) 0.008260155 3.470132e-01
## prs_scaled 0.462734925 2.489029e-01
## PC1 -0.002552555 9.511719e-03
## PC2 -0.009801941 1.121935e-02
## PC3 -0.003871033 1.689315e-02
## PC4 0.002685681 9.041623e-03
## PC5 -0.001999965 5.654077e-03
## PC6 -0.040135343 1.601504e-02
## PC7 -0.006380204 1.072084e-02
## PC8 0.018868195 1.240621e-02
## PC9 -0.003638269 8.300298e-03
## PC10 -0.020522066 1.587645e-02
## HRT.ever1 0.106212346 6.863169e-02
## agegroups[50,60) 0.404696644 2.398028e-01
## agegroups[60,70) 0.548401751 2.404813e-01
## agegroups[70,80) 0.498258381 4.824690e-01
## n.children.scale -0.084219246 5.251027e-02
## birth.x 0.025849019 4.651104e-02
## birth.y 0.003866377 5.506817e-02
## age.firstbirth.group[25,35) 0.016437898 7.876510e-02
## age.firstbirth.group[35,80) 0.260007977 1.696139e-01
## age.firstbirth.group[80,1e+03) -0.165231548 1.505095e-01
## height.scale 0.083879912 3.442054e-02
## age.menarche.scale 0.027495427 3.362473e-02
## age.menopause.scale 0.091853321 3.430845e-02
## length.oc.scale -0.002853642 3.425966e-02
## BMI.scale 0.140799613 3.441024e-02
## assessment_center10003 -0.907901843 9.730490e-01
## assessment_center11002 -0.794653476 2.766786e-01
## assessment_center11003 -0.572683907 2.913205e-01
## assessment_center11004 -0.627713208 2.821625e-01
## assessment_center11005 -0.566219723 2.835295e-01
## assessment_center11006 -0.659979986 2.693549e-01
## assessment_center11007 -0.509679603 2.535954e-01
## assessment_center11008 -0.603107201 2.525945e-01
## assessment_center11009 -0.556675326 2.537102e-01
## assessment_center11010 -0.784519512 2.443396e-01
## assessment_center11011 -0.649556236 2.470902e-01
## assessment_center11012 -0.859819191 3.116595e-01
## assessment_center11013 -0.805985131 2.519570e-01
## assessment_center11014 -1.015569554 2.594015e-01
## assessment_center11016 -0.688411115 2.470628e-01
## assessment_center11017 -0.872962357 2.749402e-01
## assessment_center11018 -1.131530426 2.767520e-01
## assessment_center11020 -1.026225978 2.687791e-01
## assessment_center11021 -0.977117327 2.690906e-01
## assessment_center11022 -0.863385349 5.254582e-01
## assessment_center11023 -13.879574550 2.518714e+02
## alcohol 0.235770877 8.172890e-02
## prs_scaled:HRT.ever1 -0.047536994 7.151213e-02
## prs_scaled:birth.x -0.090084658 3.993376e-02
## prs_scaled:birth.y -0.014453339 4.136727e-02
## prs_scaled:length.oc.scale -0.032203472 3.618277e-02
## prs_scaled:age.menopause.scale -0.014892211 3.592411e-02
## prs_scaled:age.menarche.scale 0.018043250 3.563105e-02
## prs_scaled:BMI.scale 0.023374515 3.669647e-02
## prs_scaled:agegroups[50,60) 0.136294825 2.432236e-01
## prs_scaled:agegroups[60,70) 0.119744835 2.431940e-01
## prs_scaled:agegroups[70,80) -0.791308929 5.118362e-01
## prs_scaled:alcohol -0.121363525 8.640887e-02
## prs_scaled:height.scale -0.030653526 3.613488e-02
## prs_scaled:n.children.scale -0.035647760 5.574318e-02
## prs_scaled:age.firstbirth.group[25,35) 0.083487651 8.209140e-02
## prs_scaled:age.firstbirth.group[35,80) -0.372146454 1.699289e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -0.121637151 1.592475e-01
## z value Pr(>|z|)
## (Intercept) 0.02380358 9.810093e-01
## prs_scaled 1.85909838 6.301319e-02
## PC1 -0.26835897 7.884230e-01
## PC2 -0.87366376 3.823014e-01
## PC3 -0.22914813 8.187538e-01
## PC4 0.29703529 7.664396e-01
## PC5 -0.35372087 7.235481e-01
## PC6 -2.50610393 1.220697e-02
## PC7 -0.59512149 5.517623e-01
## PC8 1.52086640 1.282934e-01
## PC9 -0.43832985 6.611472e-01
## PC10 -1.29261034 1.961459e-01
## HRT.ever1 1.54756996 1.217259e-01
## agegroups[50,60) 1.68762240 9.148374e-02
## agegroups[60,70) 2.28043404 2.258196e-02
## agegroups[70,80) 1.03272617 3.017321e-01
## n.children.scale -1.60386237 1.087444e-01
## birth.x 0.55576095 5.783743e-01
## birth.y 0.07021074 9.440259e-01
## age.firstbirth.group[25,35) 0.20869519 8.346862e-01
## age.firstbirth.group[35,80) 1.53293999 1.252906e-01
## age.firstbirth.group[80,1e+03) -1.09781444 2.722855e-01
## height.scale 2.43691415 1.481320e-02
## age.menarche.scale 0.81771455 4.135202e-01
## age.menopause.scale 2.67727970 7.422264e-03
## length.oc.scale -0.08329452 9.336174e-01
## BMI.scale 4.09179344 4.280499e-05
## assessment_center10003 -0.93304841 3.507950e-01
## assessment_center11002 -2.87211747 4.077314e-03
## assessment_center11003 -1.96582088 4.931930e-02
## assessment_center11004 -2.22465127 2.610466e-02
## assessment_center11005 -1.99704017 4.582082e-02
## assessment_center11006 -2.45022422 1.427673e-02
## assessment_center11007 -2.00981394 4.445089e-02
## assessment_center11008 -2.38764945 1.695651e-02
## assessment_center11009 -2.19413851 2.822545e-02
## assessment_center11010 -3.21077515 1.323775e-03
## assessment_center11011 -2.62882236 8.568111e-03
## assessment_center11012 -2.75884173 5.800662e-03
## assessment_center11013 -3.19889906 1.379535e-03
## assessment_center11014 -3.91504839 9.038608e-05
## assessment_center11016 -2.78638160 5.330009e-03
## assessment_center11017 -3.17509922 1.497853e-03
## assessment_center11018 -4.08860801 4.339695e-05
## assessment_center11020 -3.81810187 1.344824e-04
## assessment_center11021 -3.63118399 2.821240e-04
## assessment_center11022 -1.64310946 1.003603e-01
## assessment_center11023 -0.05510580 9.560542e-01
## alcohol 2.88479200 3.916723e-03
## prs_scaled:HRT.ever1 -0.66474031 5.062166e-01
## prs_scaled:birth.x -2.25585219 2.407989e-02
## prs_scaled:birth.y -0.34939069 7.267960e-01
## prs_scaled:length.oc.scale -0.89002234 3.734539e-01
## prs_scaled:age.menopause.scale -0.41454643 6.784740e-01
## prs_scaled:age.menarche.scale 0.50639125 6.125820e-01
## prs_scaled:BMI.scale 0.63696904 5.241450e-01
## prs_scaled:agegroups[50,60) 0.56036836 5.752282e-01
## prs_scaled:agegroups[60,70) 0.49238406 6.224479e-01
## prs_scaled:agegroups[70,80) -1.54601996 1.220997e-01
## prs_scaled:alcohol -1.40452632 1.601622e-01
## prs_scaled:height.scale -0.84830849 3.962662e-01
## prs_scaled:n.children.scale -0.63949993 5.224978e-01
## prs_scaled:age.firstbirth.group[25,35) 1.01700846 3.091494e-01
## prs_scaled:age.firstbirth.group[35,80) -2.19001302 2.852329e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -0.76382434 4.449719e-01
fit_normal.coordinate2$res_glm
## Estimate Std. Error
## (Intercept) 0.084099113 3.543370e-01
## prs_scaled 0.539253770 2.606993e-01
## PC1 -0.002163022 9.475977e-03
## PC2 -0.010132590 1.120552e-02
## PC3 -0.003428894 1.689114e-02
## PC4 0.003311438 9.043707e-03
## PC5 -0.002417363 5.659955e-03
## PC6 -0.041077883 1.603872e-02
## PC7 -0.007117651 1.073552e-02
## PC8 0.018207167 1.243182e-02
## PC9 -0.004065519 8.307971e-03
## PC10 -0.021170482 1.589182e-02
## HRT.ever1 0.109869979 6.885802e-02
## agegroups[50,60) 0.410361275 2.399195e-01
## agegroups[60,70) 0.539542033 2.405337e-01
## agegroups[70,80) 0.483933724 4.829253e-01
## n.children.scale -0.080850512 5.250915e-02
## birth.x 0.024253020 4.654079e-02
## birth.y 0.004156738 5.510173e-02
## age.firstbirth.group[25,35) 0.019211589 7.882071e-02
## age.firstbirth.group[35,80) 0.263991308 1.697172e-01
## age.firstbirth.group[80,1e+03) -0.173358103 1.508467e-01
## height.scale 0.084798118 3.444708e-02
## age.menarche.scale 0.026891753 3.364506e-02
## age.menopause.scale 0.092469164 3.434733e-02
## factor(oc.cate2)1 -0.122010945 8.895405e-02
## factor(oc.cate2)2 -0.049753651 9.381845e-02
## BMI.scale 0.141672313 3.443464e-02
## assessment_center10003 -0.920777501 9.721551e-01
## assessment_center11002 -0.798984660 2.766144e-01
## assessment_center11003 -0.577172610 2.913421e-01
## assessment_center11004 -0.641975926 2.823466e-01
## assessment_center11005 -0.570069494 2.835443e-01
## assessment_center11006 -0.671918074 2.693501e-01
## assessment_center11007 -0.508594474 2.536176e-01
## assessment_center11008 -0.607497112 2.527437e-01
## assessment_center11009 -0.554783204 2.537570e-01
## assessment_center11010 -0.790002809 2.442424e-01
## assessment_center11011 -0.656251556 2.470950e-01
## assessment_center11012 -0.863436322 3.117450e-01
## assessment_center11013 -0.808730749 2.518993e-01
## assessment_center11014 -1.014651609 2.593691e-01
## assessment_center11016 -0.692904889 2.470503e-01
## assessment_center11017 -0.878687956 2.750220e-01
## assessment_center11018 -1.138356662 2.766618e-01
## assessment_center11020 -1.030238263 2.688831e-01
## assessment_center11021 -0.983779561 2.691310e-01
## assessment_center11022 -0.874401715 5.265075e-01
## assessment_center11023 -13.909880108 2.529276e+02
## alcohol 0.241331336 8.183928e-02
## prs_scaled:HRT.ever1 -0.042648114 7.164019e-02
## prs_scaled:birth.x -0.092821154 3.994858e-02
## prs_scaled:birth.y -0.017282810 4.139910e-02
## prs_scaled:factor(oc.cate2)1 -0.053874050 9.280338e-02
## prs_scaled:factor(oc.cate2)2 -0.130461755 9.808540e-02
## prs_scaled:age.menopause.scale -0.016202964 3.596159e-02
## prs_scaled:age.menarche.scale 0.017115264 3.569845e-02
## prs_scaled:BMI.scale 0.023930049 3.670429e-02
## prs_scaled:agegroups[50,60) 0.127397630 2.429625e-01
## prs_scaled:agegroups[60,70) 0.100806963 2.432399e-01
## prs_scaled:agegroups[70,80) -0.814848646 5.131527e-01
## prs_scaled:alcohol -0.117001891 8.654854e-02
## prs_scaled:height.scale -0.028138773 3.619028e-02
## prs_scaled:n.children.scale -0.033707284 5.578834e-02
## prs_scaled:age.firstbirth.group[25,35) 0.083914662 8.216649e-02
## prs_scaled:age.firstbirth.group[35,80) -0.369853170 1.702754e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -0.120434312 1.605752e-01
## z value Pr(>|z|)
## (Intercept) 0.23734220 8.123913e-01
## prs_scaled 2.06848956 3.859401e-02
## PC1 -0.22826378 8.194412e-01
## PC2 -0.90424992 3.658629e-01
## PC3 -0.20299960 8.391353e-01
## PC4 0.36615934 7.142462e-01
## PC5 -0.42709925 6.693070e-01
## PC6 -2.56116934 1.043205e-02
## PC7 -0.66300031 5.073304e-01
## PC8 1.46456165 1.430406e-01
## PC9 -0.48935163 6.245928e-01
## PC10 -1.33216263 1.828068e-01
## HRT.ever1 1.59560181 1.105777e-01
## agegroups[50,60) 1.71041233 8.718965e-02
## agegroups[60,70) 2.24310352 2.489014e-02
## agegroups[70,80) 1.00208816 3.163010e-01
## n.children.scale -1.53974150 1.236234e-01
## birth.x 0.52111323 6.022879e-01
## birth.y 0.07543753 9.398666e-01
## age.firstbirth.group[25,35) 0.24373783 8.074339e-01
## age.firstbirth.group[35,80) 1.55547783 1.198323e-01
## age.firstbirth.group[80,1e+03) -1.14923352 2.504597e-01
## height.scale 2.46169252 1.382832e-02
## age.menarche.scale 0.79927784 4.241293e-01
## age.menopause.scale 2.69217905 7.098682e-03
## factor(oc.cate2)1 -1.37161773 1.701825e-01
## factor(oc.cate2)2 -0.53031842 5.958912e-01
## BMI.scale 4.11423865 3.884594e-05
## assessment_center10003 -0.94715087 3.435619e-01
## assessment_center11002 -2.88844209 3.871553e-03
## assessment_center11003 -1.98108221 4.758205e-02
## assessment_center11004 -2.27371603 2.298307e-02
## assessment_center11005 -2.01051296 4.437693e-02
## assessment_center11006 -2.49459026 1.261027e-02
## assessment_center11007 -2.00535974 4.492460e-02
## assessment_center11008 -2.40360895 1.623413e-02
## assessment_center11009 -2.18627730 2.879532e-02
## assessment_center11010 -3.23450295 1.218547e-03
## assessment_center11011 -2.65586693 7.910482e-03
## assessment_center11012 -2.76968791 5.611003e-03
## assessment_center11013 -3.21053180 1.324896e-03
## assessment_center11014 -3.91199899 9.153530e-05
## assessment_center11016 -2.80471213 5.036154e-03
## assessment_center11017 -3.19497385 1.398435e-03
## assessment_center11018 -4.11461527 3.878257e-05
## assessment_center11020 -3.83154696 1.273401e-04
## assessment_center11021 -3.65539303 2.567883e-04
## assessment_center11022 -1.66075827 9.676201e-02
## assessment_center11023 -0.05499551 9.561420e-01
## alcohol 2.94884465 3.189643e-03
## prs_scaled:HRT.ever1 -0.59530989 5.516363e-01
## prs_scaled:birth.x -2.32351558 2.015147e-02
## prs_scaled:birth.y -0.41746824 6.763359e-01
## prs_scaled:factor(oc.cate2)1 -0.58051821 5.615652e-01
## prs_scaled:factor(oc.cate2)2 -1.33008330 1.834908e-01
## prs_scaled:age.menopause.scale -0.45056304 6.523045e-01
## prs_scaled:age.menarche.scale 0.47943999 6.316256e-01
## prs_scaled:BMI.scale 0.65196874 5.144213e-01
## prs_scaled:agegroups[50,60) 0.52435110 6.000344e-01
## prs_scaled:agegroups[60,70) 0.41443436 6.785560e-01
## prs_scaled:agegroups[70,80) -1.58792631 1.123030e-01
## prs_scaled:alcohol -1.35186444 1.764187e-01
## prs_scaled:height.scale -0.77752305 4.368502e-01
## prs_scaled:n.children.scale -0.60419939 5.457111e-01
## prs_scaled:age.firstbirth.group[25,35) 1.02127593 3.071237e-01
## prs_scaled:age.firstbirth.group[35,80) -2.17208791 2.984903e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -0.75001818 4.532438e-01
fit_normal.coordinate3$res_glm
## Estimate Std. Error
## (Intercept) 9.592044e-02 3.546142e-01
## prs_scaled 5.434897e-01 2.585761e-01
## PC1 -1.849708e-03 9.464514e-03
## PC2 -1.048159e-02 1.122079e-02
## PC3 -2.669243e-03 1.692696e-02
## PC4 3.509450e-03 9.055153e-03
## PC5 -2.874827e-03 5.669129e-03
## PC6 -4.150908e-02 1.609610e-02
## PC7 -7.014964e-03 1.075969e-02
## PC8 1.805324e-02 1.246472e-02
## PC9 -4.205615e-03 8.316995e-03
## PC10 -2.128389e-02 1.591193e-02
## HRT.ever1 1.119814e-01 6.891983e-02
## agegroups[50,60) 4.011869e-01 2.401393e-01
## agegroups[60,70) 5.237160e-01 2.408743e-01
## agegroups[70,80) 4.522265e-01 4.833021e-01
## n.children.scale -8.193791e-02 5.259468e-02
## birth.x 2.400648e-02 4.658974e-02
## birth.y 6.255068e-04 5.514362e-02
## age.firstbirth.group[25,35) 1.698120e-02 7.888473e-02
## age.firstbirth.group[35,80) 2.666510e-01 1.699352e-01
## age.firstbirth.group[80,1e+03) -1.734104e-01 1.509869e-01
## height.scale 8.385630e-02 3.448699e-02
## age.menarche.scale 2.778278e-02 3.368448e-02
## age.menopause.scale 9.467130e-02 3.439286e-02
## factor(oc.cate3)1 -1.148840e-01 1.013758e-01
## factor(oc.cate3)2 -1.334059e-01 1.035384e-01
## factor(oc.cate3)3 3.558564e-02 1.111321e-01
## factor(oc.cate3)4 -1.194039e-01 1.078383e-01
## BMI.scale 1.413105e-01 3.445894e-02
## assessment_center10003 -9.549665e-01 9.747334e-01
## assessment_center11002 -7.945980e-01 2.768132e-01
## assessment_center11003 -5.749387e-01 2.918730e-01
## assessment_center11004 -6.320929e-01 2.826409e-01
## assessment_center11005 -5.620557e-01 2.838579e-01
## assessment_center11006 -6.728585e-01 2.694865e-01
## assessment_center11007 -5.063815e-01 2.538320e-01
## assessment_center11008 -5.951811e-01 2.530042e-01
## assessment_center11009 -5.472708e-01 2.540400e-01
## assessment_center11010 -7.874633e-01 2.445656e-01
## assessment_center11011 -6.530683e-01 2.473650e-01
## assessment_center11012 -8.684709e-01 3.118907e-01
## assessment_center11013 -8.027725e-01 2.521281e-01
## assessment_center11014 -1.006256e+00 2.595541e-01
## assessment_center11016 -6.882193e-01 2.472351e-01
## assessment_center11017 -8.790774e-01 2.752101e-01
## assessment_center11018 -1.129544e+00 2.769844e-01
## assessment_center11020 -1.031703e+00 2.689788e-01
## assessment_center11021 -9.788918e-01 2.692612e-01
## assessment_center11022 -8.662371e-01 5.265371e-01
## assessment_center11023 -1.393005e+01 2.546562e+02
## alcohol 2.462156e-01 8.197299e-02
## prs_scaled:HRT.ever1 -4.514183e-02 7.173930e-02
## prs_scaled:birth.x -9.582476e-02 4.007790e-02
## prs_scaled:birth.y -1.556683e-02 4.145647e-02
## prs_scaled:factor(oc.cate3)1 -2.942689e-02 1.062434e-01
## prs_scaled:factor(oc.cate3)2 -7.858976e-02 1.078889e-01
## prs_scaled:factor(oc.cate3)3 -2.203162e-01 1.161664e-01
## prs_scaled:factor(oc.cate3)4 -5.922072e-02 1.133993e-01
## prs_scaled:age.menopause.scale -1.874488e-02 3.602656e-02
## prs_scaled:age.menarche.scale 1.582781e-02 3.575517e-02
## prs_scaled:BMI.scale 2.418313e-02 3.671342e-02
## prs_scaled:agegroups[50,60) 1.261065e-01 2.408419e-01
## prs_scaled:agegroups[60,70) 9.988798e-02 2.408434e-01
## prs_scaled:agegroups[70,80) -8.107028e-01 5.123439e-01
## prs_scaled:alcohol -1.218825e-01 8.660897e-02
## prs_scaled:height.scale -2.634636e-02 3.622962e-02
## prs_scaled:n.children.scale -3.387916e-02 5.598839e-02
## prs_scaled:age.firstbirth.group[25,35) 9.074475e-02 8.229384e-02
## prs_scaled:age.firstbirth.group[35,80) -3.776702e-01 1.707841e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -1.232166e-01 1.609637e-01
## z value Pr(>|z|)
## (Intercept) 0.27049241 7.867815e-01
## prs_scaled 2.10185629 3.556587e-02
## PC1 -0.19543615 8.450515e-01
## PC2 -0.93412263 3.502406e-01
## PC3 -0.15769182 8.746996e-01
## PC4 0.38756388 6.983388e-01
## PC5 -0.50710209 6.120832e-01
## PC6 -2.57882821 9.913608e-03
## PC7 -0.65196688 5.144225e-01
## PC8 1.44834711 1.475200e-01
## PC9 -0.50566517 6.130917e-01
## PC10 -1.33760598 1.810249e-01
## HRT.ever1 1.62480693 1.042037e-01
## agegroups[50,60) 1.67064251 9.479231e-02
## agegroups[60,70) 2.17422968 2.968789e-02
## agegroups[70,80) 0.93570164 3.494268e-01
## n.children.scale -1.55791258 1.192540e-01
## birth.x 0.51527395 6.063616e-01
## birth.y 0.01134323 9.909496e-01
## age.firstbirth.group[25,35) 0.21526601 8.295599e-01
## age.firstbirth.group[35,80) 1.56913315 1.166169e-01
## age.firstbirth.group[80,1e+03) -1.14851264 2.507570e-01
## height.scale 2.43153471 1.503501e-02
## age.menarche.scale 0.82479469 4.094882e-01
## age.menopause.scale 2.75264366 5.911620e-03
## factor(oc.cate3)1 -1.13324861 2.571099e-01
## factor(oc.cate3)2 -1.28846839 1.975830e-01
## factor(oc.cate3)3 0.32021034 7.488089e-01
## factor(oc.cate3)4 -1.10724986 2.681859e-01
## BMI.scale 4.10083614 4.116600e-05
## assessment_center10003 -0.97972076 3.272240e-01
## assessment_center11002 -2.87052097 4.097960e-03
## assessment_center11003 -1.96982471 4.885846e-02
## assessment_center11004 -2.23638130 2.532681e-02
## assessment_center11005 -1.98006001 4.769679e-02
## assessment_center11006 -2.49681737 1.253135e-02
## assessment_center11007 -1.99494731 4.604863e-02
## assessment_center11008 -2.35245535 1.864993e-02
## assessment_center11009 -2.15427049 3.121897e-02
## assessment_center11010 -3.21984534 1.282598e-03
## assessment_center11011 -2.64010016 8.288153e-03
## assessment_center11012 -2.78453604 5.360436e-03
## assessment_center11013 -3.18398637 1.452619e-03
## assessment_center11014 -3.87686477 1.058111e-04
## assessment_center11016 -2.78366303 5.374884e-03
## assessment_center11017 -3.19420477 1.402166e-03
## assessment_center11018 -4.07800783 4.542324e-05
## assessment_center11020 -3.83562987 1.252429e-04
## assessment_center11021 -3.63547242 2.774717e-04
## assessment_center11022 -1.64515876 9.993708e-02
## assessment_center11023 -0.05470142 9.563763e-01
## alcohol 3.00361825 2.667899e-03
## prs_scaled:HRT.ever1 -0.62924829 5.291865e-01
## prs_scaled:birth.x -2.39096255 1.680427e-02
## prs_scaled:birth.y -0.37549832 7.072899e-01
## prs_scaled:factor(oc.cate3)1 -0.27697625 7.817983e-01
## prs_scaled:factor(oc.cate3)2 -0.72843239 4.663489e-01
## prs_scaled:factor(oc.cate3)3 -1.89655745 5.788637e-02
## prs_scaled:factor(oc.cate3)4 -0.52223187 6.015089e-01
## prs_scaled:age.menopause.scale -0.52030721 6.028495e-01
## prs_scaled:age.menarche.scale 0.44267185 6.580031e-01
## prs_scaled:BMI.scale 0.65869995 5.100885e-01
## prs_scaled:agegroups[50,60) 0.52360678 6.005521e-01
## prs_scaled:agegroups[60,70) 0.41474246 6.783304e-01
## prs_scaled:agegroups[70,80) -1.58234112 1.135717e-01
## prs_scaled:alcohol -1.40727352 1.593463e-01
## prs_scaled:height.scale -0.72720499 4.671004e-01
## prs_scaled:n.children.scale -0.60511050 5.451056e-01
## prs_scaled:age.firstbirth.group[25,35) 1.10269201 2.701609e-01
## prs_scaled:age.firstbirth.group[35,80) -2.21139022 2.700883e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -0.76549335 4.439778e-01
summary.caseonly=function (parms, sd, sided = 2)
{
if (sided != 1)
sided <- 2
cols <- c("Estimate", "Std.Error", "Z.value", "Pvalue")
n <- length(parms)
ret <- matrix(data = NA, nrow = n, ncol = 4)
pnames <- c("prs",paste0("prs:",names(parms)[-1]))
rownames(ret) <- pnames
colnames(ret) <- cols
ret[, 1] <- parms
if (is.null(pnames))
pnames <- 1:n
cov <- sd
ret[, 2] <- cov
ret[, 3] <- parms/cov
ret[, 4] <- sided * pnorm(abs(ret[, 3]), lower.tail = FALSE)
ret
}
dat_caseonly=dat_test_casecontrol.coordinate[which(dat_test_casecontrol.coordinate$breast_cancer==1),]
fit_caseonly <- lm(prs_scaled~PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+length.oc.scale+BMI.scale+assessment_center+alcohol,data=dat_caseonly)
beta_int=fit_caseonly$coefficients[-1]/(sd(fit_caseonly$residuals))^2
sd_int=summary(fit_caseonly)$coef[-1,2]/(sd(fit_caseonly$residuals))^2
mean_prs=mean(dat_test_complete$prs_scaled)
beta_prs=(fit_caseonly$coefficients[1]-mean_prs)/(sd(fit_caseonly$residuals))^2
sd_prs= sqrt(( (summary(fit_caseonly)$coef[1,2])^2 +(sd(fit_caseonly$residuals))^2/dim(dat_test_complete)[1]) / (sd(fit_caseonly$residuals))^4)
res_caseonly_post=summary.caseonly(parms = c(beta_prs,beta_int),sd=c(sd_prs,sd_int))
print(res_caseonly_post)
## Estimate Std.Error Z.value
## prs 0.3728294232 0.252853609 1.47448725
## prs:PC1 -0.0013406026 0.009799870 -0.13679799
## prs:PC2 0.0040196087 0.008794805 0.45704352
## prs:PC3 -0.0124403709 0.012104001 -1.02778996
## prs:PC4 -0.0159482490 0.006812588 -2.34099713
## prs:PC5 -0.0053440327 0.004052694 -1.31863718
## prs:PC6 -0.0037472430 0.013533251 -0.27689156
## prs:PC7 0.0046584632 0.007807159 0.59669119
## prs:PC8 0.0083720993 0.009819084 0.85263550
## prs:PC9 0.0064857885 0.005917769 1.09598541
## prs:PC10 0.0092619437 0.011417671 0.81119378
## prs:HRT.ever1 -0.0278167796 0.048365028 -0.57514242
## prs:agegroups[50,60) -0.0712761694 0.191323443 -0.37254279
## prs:agegroups[60,70) -0.0802104321 0.191098749 -0.41973290
## prs:agegroups[70,80) -0.6629463398 0.358763078 -1.84786668
## prs:n.children.scale 0.0106798315 0.037500287 0.28479333
## prs:birth.x -0.0911838656 0.032915548 -2.77023689
## prs:birth.y -0.0077704336 0.038827275 -0.20012823
## prs:age.firstbirth.group[25,35) 0.0824116394 0.055935308 1.47333844
## prs:age.firstbirth.group[35,80) -0.1489171292 0.116058444 -1.28312189
## prs:age.firstbirth.group[80,1e+03) -0.0373014572 0.108486179 -0.34383603
## prs:height.scale -0.0163562863 0.024059436 -0.67982834
## prs:age.menarche.scale -0.0114750268 0.023099427 -0.49676672
## prs:age.menopause.scale -0.0008313827 0.024108716 -0.03448474
## prs:length.oc.scale -0.0501674937 0.024349621 -2.06029877
## prs:BMI.scale -0.0140314662 0.024984648 -0.56160351
## prs:assessment_center10003 -0.3698482992 0.751905360 -0.49188145
## prs:assessment_center11002 -0.0132612901 0.178675116 -0.07422013
## prs:assessment_center11003 0.0144130623 0.185067630 0.07787997
## prs:assessment_center11004 -0.0700282341 0.178696029 -0.39188467
## prs:assessment_center11005 0.0055300825 0.178774441 0.03093329
## prs:assessment_center11006 0.0450617140 0.171118409 0.26333645
## prs:assessment_center11007 -0.0104247430 0.157206880 -0.06631226
## prs:assessment_center11008 -0.0998227445 0.157450547 -0.63399427
## prs:assessment_center11009 -0.0337616535 0.157028028 -0.21500400
## prs:assessment_center11010 -0.2010175695 0.152666291 -1.31671221
## prs:assessment_center11011 -0.0956082806 0.154248338 -0.61983346
## prs:assessment_center11012 0.1495237490 0.209584471 0.71342952
## prs:assessment_center11013 0.1015525225 0.158175239 0.64202541
## prs:assessment_center11014 -0.0851876884 0.167958370 -0.50719526
## prs:assessment_center11016 -0.0893563686 0.154111000 -0.57981824
## prs:assessment_center11017 -0.0613602476 0.178677402 -0.34341359
## prs:assessment_center11018 0.0140224545 0.184764848 0.07589352
## prs:assessment_center11020 -0.0923511493 0.176740308 -0.52252455
## prs:assessment_center11021 0.0569829084 0.174871261 0.32585634
## prs:assessment_center11022 0.3766075671 0.346484121 1.08694034
## prs:alcohol -0.0908146015 0.059297025 -1.53152038
## Pvalue
## prs 0.140350447
## prs:PC1 0.891190473
## prs:PC2 0.647639769
## prs:PC3 0.304048638
## prs:PC4 0.019232315
## prs:PC5 0.187290439
## prs:PC6 0.781863372
## prs:PC7 0.550713579
## prs:PC8 0.393861469
## prs:PC9 0.273085160
## prs:PC10 0.417254399
## prs:HRT.ever1 0.565194980
## prs:agegroups[50,60) 0.709488758
## prs:agegroups[60,70) 0.674680587
## prs:agegroups[70,80) 0.064621631
## prs:n.children.scale 0.775802481
## prs:birth.x 0.005601554
## prs:birth.y 0.841380297
## prs:age.firstbirth.group[25,35) 0.140659801
## prs:age.firstbirth.group[35,80) 0.199449377
## prs:age.firstbirth.group[80,1e+03) 0.730969602
## prs:height.scale 0.496613163
## prs:age.menarche.scale 0.619353565
## prs:age.menopause.scale 0.972490613
## prs:length.oc.scale 0.039369987
## prs:BMI.scale 0.574386188
## prs:assessment_center10003 0.622803152
## prs:assessment_center11002 0.940835230
## prs:assessment_center11003 0.937923529
## prs:assessment_center11004 0.695143431
## prs:assessment_center11005 0.975322737
## prs:assessment_center11006 0.792291269
## prs:assessment_center11007 0.947129225
## prs:assessment_center11008 0.526084562
## prs:assessment_center11009 0.829764203
## prs:assessment_center11010 0.187935108
## prs:assessment_center11011 0.535367440
## prs:assessment_center11012 0.475580009
## prs:assessment_center11013 0.520856686
## prs:assessment_center11014 0.612017823
## prs:assessment_center11016 0.562037197
## prs:assessment_center11017 0.731287339
## prs:assessment_center11018 0.939503813
## prs:assessment_center11020 0.601305160
## prs:assessment_center11021 0.744533052
## prs:assessment_center11022 0.277063179
## prs:alcohol 0.125640835
fit_caseonly <- lm(prs_scaled~HRT.ever+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+age.menopause.scale+length.oc.scale+BMI.scale+alcohol,data=dat_caseonly)
beta_int=fit_caseonly$coefficients[-1]/(sd(fit_caseonly$residuals))^2
sd_int=summary(fit_caseonly)$coef[-1,2]/(sd(fit_caseonly$residuals))^2
beta_prs=(fit_caseonly$coefficients[1]-mean_prs)/(sd(fit_caseonly$residuals))^2
sd_prs= sqrt(( (summary(fit_caseonly)$coef[1,2])^2 +(sd(fit_caseonly$residuals))^2/dim(dat_test_complete)[1]) / (sd(fit_caseonly$residuals))^4)
res_caseonly=summary.caseonly(parms = c(beta_prs,beta_int),sd=c(sd_prs,sd_int))
print(res_caseonly)
## Estimate Std.Error Z.value
## prs 0.338447886 0.19289246 1.7545937
## prs:HRT.ever1 -0.018313578 0.04702643 -0.3894316
## prs:agegroups[50,60) -0.035260410 0.18731082 -0.1882454
## prs:agegroups[60,70) -0.041579990 0.18703791 -0.2223078
## prs:agegroups[70,80) -0.587543027 0.34991132 -1.6791198
## prs:n.children.scale 0.009730859 0.03661136 0.2657880
## prs:birth.x -0.060790336 0.02587224 -2.3496355
## prs:birth.y -0.024643090 0.02574363 -0.9572498
## prs:age.firstbirth.group[25,35) 0.085125919 0.05421099 1.5702704
## prs:age.firstbirth.group[35,80) -0.150253018 0.11301486 -1.3294979
## prs:age.firstbirth.group[80,1e+03) -0.041552281 0.10526615 -0.3947355
## prs:height.scale -0.011844765 0.02337593 -0.5067078
## prs:age.menarche.scale -0.010913432 0.02259508 -0.4830003
## prs:age.menopause.scale 0.003841007 0.02353369 0.1632131
## prs:length.oc.scale -0.049364503 0.02368247 -2.0844324
## prs:BMI.scale -0.015010495 0.02439820 -0.6152296
## prs:alcohol -0.109211341 0.05767745 -1.8934843
## Pvalue
## prs 0.07932883
## prs:HRT.ever1 0.69695689
## prs:agegroups[50,60) 0.85068425
## prs:agegroups[60,70) 0.82407426
## prs:agegroups[70,80) 0.09312869
## prs:n.children.scale 0.79040251
## prs:birth.x 0.01879180
## prs:birth.y 0.33844117
## prs:age.firstbirth.group[25,35) 0.11635221
## prs:age.firstbirth.group[35,80) 0.18368375
## prs:age.firstbirth.group[80,1e+03) 0.69303813
## prs:height.scale 0.61235983
## prs:age.menarche.scale 0.62909550
## prs:age.menopause.scale 0.87035063
## prs:length.oc.scale 0.03712085
## prs:BMI.scale 0.53840307
## prs:alcohol 0.05829349
For pre-menopause cohort, we also found PRS by length.oc use interaction term significant in association with breast cancer.
dat0_premeno_bc=dat0[which(dat0$menopause=="No" ),]
dat0_premeno_bc$prs_scaled=scale(dat0_premeno_bc$prs_bc,center = T,scale = T)
fit <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10, data=dat0_premeno_bc,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10, family = binomial(),
## data = dat0_premeno_bc, model = FALSE, x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.5244 -0.2109 -0.1803 -0.1504 3.3244
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -4.2259386 0.1154316 -36.610 <2e-16 ***
## prs_scaled 0.4890811 0.0346920 14.098 <2e-16 ***
## PC1 -0.0107784 0.0106381 -1.013 0.3110
## PC2 0.0046543 0.0124950 0.372 0.7095
## PC3 0.0112037 0.0164868 0.680 0.4968
## PC4 -0.0008491 0.0075349 -0.113 0.9103
## PC5 0.0006075 0.0047876 0.127 0.8990
## PC6 0.0070373 0.0111434 0.632 0.5277
## PC7 0.0071911 0.0076283 0.943 0.3458
## PC8 -0.0174168 0.0090184 -1.931 0.0535 .
## PC9 -0.0019333 0.0078675 -0.246 0.8059
## PC10 -0.0002838 0.0137931 -0.021 0.9836
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 8515.3 on 46815 degrees of freedom
## Residual deviance: 8309.0 on 46804 degrees of freedom
## AIC: 8333
##
## Number of Fisher Scoring iterations: 7
exp(0.4890811)
## [1] 1.630817
colnames(dat0_premeno_bc)[7]="age.menarche"
dat0_premeno_bc$n.children=as.numeric(as.character(dat0_premeno_bc$n.children))
dat0_premeno_bc$age.menopause=as.numeric(as.character(dat0_premeno_bc$age.menopause))
dat0_premeno_bc$n.children[which(dat0_premeno_bc$n.children=="-3")]=NA
#winsorization
dat0_premeno_bc$n.children.win=dat0_premeno_bc$n.children
dat0_premeno_bc$n.children.win[which(dat0_premeno_bc$n.children.win>=5)]=5
dat0_premeno_bc$alcohol=NA
dat0_premeno_bc$alcohol[which(dat0_premeno_bc$AlcoholFreq=="Never" | dat0_premeno_bc$AlcoholFreq== "Special occasions only")]=0
dat0_premeno_bc$alcohol[which(dat0_premeno_bc$AlcoholFreq=="Daily or almost daily" | dat0_premeno_bc$AlcoholFreq== "Three or four times a week" |
dat0_premeno_bc$AlcoholFreq== "Once or twice a week" | dat0_premeno_bc$AlcoholFreq=="One to three times a month" )]=1
dat0_premeno_bc$age.firstbirth=as.numeric(as.character(dat0_premeno_bc$age.firstbirth))
dat0_premeno_bc$age.firstbirth[which(dat0_premeno_bc$age.firstbirth== -3 | dat0_premeno_bc$age.firstbirth== -4)]=NA
dat0_premeno_bc$age.firstbirth[which(dat0_premeno_bc$n.children==0)]=999
dat0_premeno_bc$age.firstbirth.group=NA
dat0_premeno_bc$age.firstbirth.group<-cut(dat0_premeno_bc$age.firstbirth, breaks=c( 0, 25,35,80,1000), right = FALSE)
dat0_premeno_bc$age.menarche[which(dat0_premeno_bc$age.menarche<0)]=NA
dat0_premeno_bc$agegroups<-cut(dat0_premeno_bc$age, breaks=c( 40, 45,50,80), right = FALSE)
dat0_premeno_bc$birth.x[which(dat0_premeno_bc$birth.x<0)]=NA
dat0_premeno_bc$birth.y[which(dat0_premeno_bc$birth.y<0)]=NA
dat0_premeno_bc$oc.cate2=NA
dat0_premeno_bc$oc.cate2[which(dat0_premeno_bc$oral.contraceptive.ever==0)]=0
dat0_premeno_bc$oc.cate2[which(dat0_premeno_bc$oral.contraceptive.ever==1 & dat0_premeno_bc$length.oc<10)]=1
dat0_premeno_bc$oc.cate2[which( dat0_premeno_bc$length.oc>=10)]=2
#more specified interval
dat0_premeno_bc$oc.cate3=NA
dat0_premeno_bc$oc.cate3[which(dat0_premeno_bc$oral.contraceptive.ever==0)]=0
dat0_premeno_bc$oc.cate3[which(dat0_premeno_bc$oral.contraceptive.ever==1 & dat0_premeno_bc$length.oc<5)]=1
dat0_premeno_bc$oc.cate3[which( dat0_premeno_bc$length.oc>=5 & dat0_premeno_bc$length.oc < 10)]=2
dat0_premeno_bc$oc.cate3[which( dat0_premeno_bc$length.oc>=10 & dat0_premeno_bc$length.oc < 15)]=3
dat0_premeno_bc$oc.cate3[which( dat0_premeno_bc$length.oc>=15 )]=4
dat_test=dat0_premeno_bc[,c("IID","prs_bc","age","age.menarche","BMI","height","n.children.win","age.firstbirth",
"breast_cancer","breast_cancer_incident","length.oc","oral.contraceptive.ever",
"assessment_center","agegroups",
"oc.cate","oc.cate2","oc.cate3" ,"alcohol","age.firstbirth.group","PC1","PC2","PC3","PC4","PC5","PC6","PC7","PC8","PC9","PC10")]
dat_test=dat_test[complete.cases(dat_test),]
table(dat_test$breast_cancer)
##
## 0 1
## 42046 777
table(dat_test$breast_cancer_incident)
##
## 0 1
## 42046 777
dim(dat_test)
## [1] 42823 29
dat_test$prs_scaled=scale(dat_test$prs_bc,center = T,scale = T)
dat_test$age.scale=scale(dat_test$age,center = T,scale=T)
dat_test$age.menarche.scale=scale(dat_test$age.menarche,center = T,scale=T)
dat_test$n.children.scale=scale(dat_test$n.children.win,center=T,scale = T)
dat_test$height.scale=scale(dat_test$height,center=T,scale = T)
dat_test$BMI.scale=scale(dat_test$BMI,center=T,scale = T)
dat_test$length.oc.scale=scale(dat_test$length.oc,center=T,scale = T)
dat_location=dat0_premeno_bc[,c("IID","birth.x","birth.y")]
dat_test=merge(dat_test,dat_location,by="IID")
dat_test$birth.x=scale(dat_test$birth.x,center=T,scale=T)
dat_test$birth.y=scale(dat_test$birth.y,center=T,scale=T)
dat_test_complete=dat_test[complete.cases(dat_test),]
table(dat_test_complete$breast_cancer)
##
## 0 1
## 37785 704
fit.int.all.premeno <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+length.oc.scale+BMI.scale+relevel(factor(dat_test_complete$assessment_center),ref = "11001")+alcohol+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:length.oc.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group, data=dat_test_complete,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit.int.all.premeno)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10 + agegroups + n.children.scale +
## birth.x + birth.y + age.firstbirth.group + height.scale +
## age.menarche.scale + length.oc.scale + BMI.scale + relevel(factor(dat_test_complete$assessment_center),
## ref = "11001") + alcohol + prs_scaled:birth.x + prs_scaled:birth.y +
## prs_scaled:length.oc.scale + prs_scaled:age.menarche.scale +
## prs_scaled:BMI.scale + prs_scaled:agegroups + prs_scaled:alcohol +
## prs_scaled:height.scale + prs_scaled:n.children.scale + prs_scaled:age.firstbirth.group,
## family = binomial(), data = dat_test_complete, model = FALSE,
## x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.7079 -0.2142 -0.1762 -0.1394 3.4253
##
## Coefficients:
## Estimate
## (Intercept) -4.976e+00
## prs_scaled 4.337e-01
## PC1 -2.398e-02
## PC2 -1.990e-02
## PC3 1.211e-02
## PC4 -8.805e-03
## PC5 -8.895e-04
## PC6 4.826e-02
## PC7 1.915e-02
## PC8 -2.501e-02
## PC9 9.461e-04
## PC10 8.655e-03
## agegroups[45,50) 1.934e-01
## agegroups[50,80) 1.561e-01
## n.children.scale 1.311e-01
## birth.x 6.402e-03
## birth.y 8.102e-02
## age.firstbirth.group[25,35) 3.022e-01
## age.firstbirth.group[35,80) 5.181e-01
## age.firstbirth.group[80,1e+03) 6.951e-01
## height.scale 1.051e-01
## age.menarche.scale -7.205e-03
## length.oc.scale 1.426e-01
## BMI.scale 1.894e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 4.412e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 1.683e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 3.371e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 1.273e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 6.826e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 4.104e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 2.454e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 3.878e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 1.326e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 1.189e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -8.398e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -5.414e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -7.733e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -2.828e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -2.445e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -1.908e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -7.623e-04
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -3.425e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -4.059e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -1.237e+01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -1.229e+01
## alcohol 1.758e-01
## prs_scaled:birth.x -1.455e-02
## prs_scaled:birth.y -2.874e-03
## prs_scaled:length.oc.scale -8.066e-02
## prs_scaled:age.menarche.scale -3.156e-02
## prs_scaled:BMI.scale -2.976e-02
## prs_scaled:agegroups[45,50) 2.942e-02
## prs_scaled:agegroups[50,80) 1.462e-01
## prs_scaled:alcohol 5.734e-02
## prs_scaled:height.scale 9.110e-04
## prs_scaled:n.children.scale -3.516e-03
## prs_scaled:age.firstbirth.group[25,35) -4.107e-02
## prs_scaled:age.firstbirth.group[35,80) 2.475e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -5.703e-02
## Std. Error
## (Intercept) 3.216e-01
## prs_scaled 1.575e-01
## PC1 1.668e-02
## PC2 1.442e-02
## PC3 1.667e-02
## PC4 8.744e-03
## PC5 6.358e-03
## PC6 2.128e-02
## PC7 1.036e-02
## PC8 1.435e-02
## PC9 1.020e-02
## PC10 1.743e-02
## agegroups[45,50) 9.558e-02
## agegroups[50,80) 1.192e-01
## n.children.scale 7.618e-02
## birth.x 5.725e-02
## birth.y 6.550e-02
## age.firstbirth.group[25,35) 1.289e-01
## age.firstbirth.group[35,80) 1.840e-01
## age.firstbirth.group[80,1e+03) 2.124e-01
## height.scale 4.363e-02
## age.menarche.scale 4.320e-02
## length.oc.scale 4.117e-02
## BMI.scale 4.373e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 1.041e+00
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 3.018e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 2.944e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 2.988e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 2.933e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 2.806e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 2.666e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 2.661e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 2.662e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 2.527e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 2.625e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 3.931e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 2.712e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 2.882e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 2.857e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 3.087e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 2.858e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 3.121e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 3.176e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 1.935e+02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 3.399e+02
## alcohol 1.237e-01
## prs_scaled:birth.x 4.387e-02
## prs_scaled:birth.y 4.236e-02
## prs_scaled:length.oc.scale 3.744e-02
## prs_scaled:age.menarche.scale 3.984e-02
## prs_scaled:BMI.scale 4.065e-02
## prs_scaled:agegroups[45,50) 8.748e-02
## prs_scaled:agegroups[50,80) 1.063e-01
## prs_scaled:alcohol 1.141e-01
## prs_scaled:height.scale 3.884e-02
## prs_scaled:n.children.scale 6.797e-02
## prs_scaled:age.firstbirth.group[25,35) 1.154e-01
## prs_scaled:age.firstbirth.group[35,80) 1.658e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 1.905e-01
## z value
## (Intercept) -15.471
## prs_scaled 2.753
## PC1 -1.437
## PC2 -1.380
## PC3 0.727
## PC4 -1.007
## PC5 -0.140
## PC6 2.267
## PC7 1.848
## PC8 -1.742
## PC9 0.093
## PC10 0.497
## agegroups[45,50) 2.023
## agegroups[50,80) 1.309
## n.children.scale 1.721
## birth.x 0.112
## birth.y 1.237
## age.firstbirth.group[25,35) 2.343
## age.firstbirth.group[35,80) 2.816
## age.firstbirth.group[80,1e+03) 3.272
## height.scale 2.409
## age.menarche.scale -0.167
## length.oc.scale 3.464
## BMI.scale 0.433
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.424
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.558
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 1.145
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.426
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.233
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 1.462
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.920
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 1.458
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.498
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.470
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -0.320
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -1.377
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -0.285
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -0.981
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -0.856
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -0.618
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -0.003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -1.097
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -1.278
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -0.064
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -0.036
## alcohol 1.422
## prs_scaled:birth.x -0.332
## prs_scaled:birth.y -0.068
## prs_scaled:length.oc.scale -2.155
## prs_scaled:age.menarche.scale -0.792
## prs_scaled:BMI.scale -0.732
## prs_scaled:agegroups[45,50) 0.336
## prs_scaled:agegroups[50,80) 1.375
## prs_scaled:alcohol 0.503
## prs_scaled:height.scale 0.023
## prs_scaled:n.children.scale -0.052
## prs_scaled:age.firstbirth.group[25,35) -0.356
## prs_scaled:age.firstbirth.group[35,80) 0.149
## prs_scaled:age.firstbirth.group[80,1e+03) -0.299
## Pr(>|z|)
## (Intercept) < 2e-16
## prs_scaled 0.005896
## PC1 0.150609
## PC2 0.167658
## PC3 0.467495
## PC4 0.313942
## PC5 0.888725
## PC6 0.023364
## PC7 0.064639
## PC8 0.081480
## PC9 0.926121
## PC10 0.619481
## agegroups[45,50) 0.043040
## agegroups[50,80) 0.190378
## n.children.scale 0.085234
## birth.x 0.910963
## birth.y 0.216094
## age.firstbirth.group[25,35) 0.019111
## age.firstbirth.group[35,80) 0.004862
## age.firstbirth.group[80,1e+03) 0.001066
## height.scale 0.016008
## age.menarche.scale 0.867540
## length.oc.scale 0.000532
## BMI.scale 0.664873
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.671803
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.577020
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 0.252143
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.670062
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.815991
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 0.143630
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.357313
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 0.144933
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.618432
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.638043
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 0.749045
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 0.168464
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 0.775530
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 0.326531
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 0.392058
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 0.536645
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 0.997872
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 0.272517
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 0.201267
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 0.949029
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 0.971162
## alcohol 0.155069
## prs_scaled:birth.x 0.740045
## prs_scaled:birth.y 0.945909
## prs_scaled:length.oc.scale 0.031191
## prs_scaled:age.menarche.scale 0.428331
## prs_scaled:BMI.scale 0.464097
## prs_scaled:agegroups[45,50) 0.736621
## prs_scaled:agegroups[50,80) 0.169269
## prs_scaled:alcohol 0.615303
## prs_scaled:height.scale 0.981289
## prs_scaled:n.children.scale 0.958749
## prs_scaled:age.firstbirth.group[25,35) 0.721988
## prs_scaled:age.firstbirth.group[35,80) 0.881325
## prs_scaled:age.firstbirth.group[80,1e+03) 0.764702
##
## (Intercept) ***
## prs_scaled **
## PC1
## PC2
## PC3
## PC4
## PC5
## PC6 *
## PC7 .
## PC8 .
## PC9
## PC10
## agegroups[45,50) *
## agegroups[50,80)
## n.children.scale .
## birth.x
## birth.y
## age.firstbirth.group[25,35) *
## age.firstbirth.group[35,80) **
## age.firstbirth.group[80,1e+03) **
## height.scale *
## age.menarche.scale
## length.oc.scale ***
## BMI.scale
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023
## alcohol
## prs_scaled:birth.x
## prs_scaled:birth.y
## prs_scaled:length.oc.scale *
## prs_scaled:age.menarche.scale
## prs_scaled:BMI.scale
## prs_scaled:agegroups[45,50)
## prs_scaled:agegroups[50,80)
## prs_scaled:alcohol
## prs_scaled:height.scale
## prs_scaled:n.children.scale
## prs_scaled:age.firstbirth.group[25,35)
## prs_scaled:age.firstbirth.group[35,80)
## prs_scaled:age.firstbirth.group[80,1e+03)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 7028.9 on 38488 degrees of freedom
## Residual deviance: 6757.4 on 38430 degrees of freedom
## AIC: 6875.4
##
## Number of Fisher Scoring iterations: 15
fit.int.all2.premeno <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+factor(oc.cate2)+BMI.scale+relevel(factor(dat_test_complete$assessment_center),ref = "11001")+alcohol+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:factor(oc.cate2)+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group, data=dat_test_complete,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit.int.all2.premeno)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10 + agegroups + n.children.scale +
## birth.x + birth.y + age.firstbirth.group + height.scale +
## age.menarche.scale + factor(oc.cate2) + BMI.scale + relevel(factor(dat_test_complete$assessment_center),
## ref = "11001") + alcohol + prs_scaled:birth.x + prs_scaled:birth.y +
## prs_scaled:factor(oc.cate2) + prs_scaled:age.menarche.scale +
## prs_scaled:BMI.scale + prs_scaled:agegroups + prs_scaled:alcohol +
## prs_scaled:height.scale + prs_scaled:n.children.scale + prs_scaled:age.firstbirth.group,
## family = binomial(), data = dat_test_complete, model = FALSE,
## x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.7631 -0.2145 -0.1761 -0.1391 3.5061
##
## Coefficients:
## Estimate
## (Intercept) -4.900e+00
## prs_scaled 4.392e-01
## PC1 -2.387e-02
## PC2 -1.943e-02
## PC3 1.215e-02
## PC4 -8.990e-03
## PC5 -1.329e-03
## PC6 4.843e-02
## PC7 1.900e-02
## PC8 -2.513e-02
## PC9 9.175e-04
## PC10 8.565e-03
## agegroups[45,50) 2.036e-01
## agegroups[50,80) 1.643e-01
## n.children.scale 1.242e-01
## birth.x 7.647e-03
## birth.y 8.093e-02
## age.firstbirth.group[25,35) 2.927e-01
## age.firstbirth.group[35,80) 4.875e-01
## age.firstbirth.group[80,1e+03) 6.554e-01
## height.scale 1.040e-01
## age.menarche.scale -6.514e-03
## factor(oc.cate2)1 -2.960e-01
## factor(oc.cate2)2 5.227e-02
## BMI.scale 1.762e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 4.706e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 1.743e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 3.353e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 1.242e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 8.003e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 4.135e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 2.523e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 3.876e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 1.311e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 1.172e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -7.703e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -5.301e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -7.699e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -2.789e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -2.470e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -1.912e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -3.562e-03
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -3.389e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -4.086e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -1.238e+01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -1.226e+01
## alcohol 1.921e-01
## prs_scaled:birth.x -1.619e-02
## prs_scaled:birth.y -2.530e-03
## prs_scaled:factor(oc.cate2)1 8.368e-02
## prs_scaled:factor(oc.cate2)2 -6.423e-02
## prs_scaled:age.menarche.scale -3.139e-02
## prs_scaled:BMI.scale -2.902e-02
## prs_scaled:agegroups[45,50) 2.540e-02
## prs_scaled:agegroups[50,80) 1.432e-01
## prs_scaled:alcohol 5.007e-02
## prs_scaled:height.scale 2.371e-03
## prs_scaled:n.children.scale 2.278e-04
## prs_scaled:age.firstbirth.group[25,35) -3.771e-02
## prs_scaled:age.firstbirth.group[35,80) 3.598e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -4.626e-02
## Std. Error
## (Intercept) 3.456e-01
## prs_scaled 1.941e-01
## PC1 1.665e-02
## PC2 1.442e-02
## PC3 1.672e-02
## PC4 8.747e-03
## PC5 6.354e-03
## PC6 2.132e-02
## PC7 1.036e-02
## PC8 1.436e-02
## PC9 1.020e-02
## PC10 1.745e-02
## agegroups[45,50) 9.564e-02
## agegroups[50,80) 1.195e-01
## n.children.scale 7.609e-02
## birth.x 5.728e-02
## birth.y 6.552e-02
## age.firstbirth.group[25,35) 1.290e-01
## age.firstbirth.group[35,80) 1.843e-01
## age.firstbirth.group[80,1e+03) 2.132e-01
## height.scale 4.360e-02
## age.menarche.scale 4.314e-02
## factor(oc.cate2)1 1.595e-01
## factor(oc.cate2)2 1.480e-01
## BMI.scale 4.366e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 1.041e+00
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 3.018e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 2.944e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 2.988e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 2.933e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 2.807e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 2.666e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 2.661e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 2.662e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 2.527e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 2.626e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 3.932e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 2.712e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 2.883e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 2.857e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 3.087e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 2.858e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 3.121e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 3.176e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 1.934e+02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 3.400e+02
## alcohol 1.240e-01
## prs_scaled:birth.x 4.387e-02
## prs_scaled:birth.y 4.237e-02
## prs_scaled:factor(oc.cate2)1 1.431e-01
## prs_scaled:factor(oc.cate2)2 1.347e-01
## prs_scaled:age.menarche.scale 3.986e-02
## prs_scaled:BMI.scale 4.064e-02
## prs_scaled:agegroups[45,50) 8.764e-02
## prs_scaled:agegroups[50,80) 1.068e-01
## prs_scaled:alcohol 1.146e-01
## prs_scaled:height.scale 3.890e-02
## prs_scaled:n.children.scale 6.790e-02
## prs_scaled:age.firstbirth.group[25,35) 1.156e-01
## prs_scaled:age.firstbirth.group[35,80) 1.662e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 1.912e-01
## z value
## (Intercept) -14.178
## prs_scaled 2.263
## PC1 -1.434
## PC2 -1.348
## PC3 0.727
## PC4 -1.028
## PC5 -0.209
## PC6 2.272
## PC7 1.833
## PC8 -1.750
## PC9 0.090
## PC10 0.491
## agegroups[45,50) 2.129
## agegroups[50,80) 1.375
## n.children.scale 1.632
## birth.x 0.134
## birth.y 1.235
## age.firstbirth.group[25,35) 2.268
## age.firstbirth.group[35,80) 2.645
## age.firstbirth.group[80,1e+03) 3.074
## height.scale 2.386
## age.menarche.scale -0.151
## factor(oc.cate2)1 -1.856
## factor(oc.cate2)2 0.353
## BMI.scale 0.403
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.452
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.577
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 1.139
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.416
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.273
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 1.473
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.946
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 1.456
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.493
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.464
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -0.293
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -1.348
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -0.284
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -0.967
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -0.864
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -0.619
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -0.012
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -1.086
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -1.286
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -0.064
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -0.036
## alcohol 1.549
## prs_scaled:birth.x -0.369
## prs_scaled:birth.y -0.060
## prs_scaled:factor(oc.cate2)1 0.585
## prs_scaled:factor(oc.cate2)2 -0.477
## prs_scaled:age.menarche.scale -0.788
## prs_scaled:BMI.scale -0.714
## prs_scaled:agegroups[45,50) 0.290
## prs_scaled:agegroups[50,80) 1.341
## prs_scaled:alcohol 0.437
## prs_scaled:height.scale 0.061
## prs_scaled:n.children.scale 0.003
## prs_scaled:age.firstbirth.group[25,35) -0.326
## prs_scaled:age.firstbirth.group[35,80) 0.216
## prs_scaled:age.firstbirth.group[80,1e+03) -0.242
## Pr(>|z|)
## (Intercept) < 2e-16
## prs_scaled 0.02361
## PC1 0.15151
## PC2 0.17780
## PC3 0.46728
## PC4 0.30406
## PC5 0.83428
## PC6 0.02308
## PC7 0.06676
## PC8 0.08006
## PC9 0.92833
## PC10 0.62351
## agegroups[45,50) 0.03329
## agegroups[50,80) 0.16918
## n.children.scale 0.10275
## birth.x 0.89379
## birth.y 0.21679
## age.firstbirth.group[25,35) 0.02334
## age.firstbirth.group[35,80) 0.00816
## age.firstbirth.group[80,1e+03) 0.00211
## height.scale 0.01705
## age.menarche.scale 0.87998
## factor(oc.cate2)1 0.06347
## factor(oc.cate2)2 0.72403
## BMI.scale 0.68660
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.65129
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.56366
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 0.25472
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.67761
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.78495
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 0.14075
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.34399
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 0.14528
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.62224
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.64274
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 0.76924
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 0.17755
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 0.77650
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 0.33330
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 0.38736
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 0.53570
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 0.99005
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 0.27760
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 0.19828
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 0.94896
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 0.97124
## alcohol 0.12133
## prs_scaled:birth.x 0.71208
## prs_scaled:birth.y 0.95239
## prs_scaled:factor(oc.cate2)1 0.55878
## prs_scaled:factor(oc.cate2)2 0.63344
## prs_scaled:age.menarche.scale 0.43097
## prs_scaled:BMI.scale 0.47520
## prs_scaled:agegroups[45,50) 0.77194
## prs_scaled:agegroups[50,80) 0.18002
## prs_scaled:alcohol 0.66222
## prs_scaled:height.scale 0.95141
## prs_scaled:n.children.scale 0.99732
## prs_scaled:age.firstbirth.group[25,35) 0.74428
## prs_scaled:age.firstbirth.group[35,80) 0.82861
## prs_scaled:age.firstbirth.group[80,1e+03) 0.80886
##
## (Intercept) ***
## prs_scaled *
## PC1
## PC2
## PC3
## PC4
## PC5
## PC6 *
## PC7 .
## PC8 .
## PC9
## PC10
## agegroups[45,50) *
## agegroups[50,80)
## n.children.scale
## birth.x
## birth.y
## age.firstbirth.group[25,35) *
## age.firstbirth.group[35,80) **
## age.firstbirth.group[80,1e+03) **
## height.scale *
## age.menarche.scale
## factor(oc.cate2)1 .
## factor(oc.cate2)2
## BMI.scale
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023
## alcohol
## prs_scaled:birth.x
## prs_scaled:birth.y
## prs_scaled:factor(oc.cate2)1
## prs_scaled:factor(oc.cate2)2
## prs_scaled:age.menarche.scale
## prs_scaled:BMI.scale
## prs_scaled:agegroups[45,50)
## prs_scaled:agegroups[50,80)
## prs_scaled:alcohol
## prs_scaled:height.scale
## prs_scaled:n.children.scale
## prs_scaled:age.firstbirth.group[25,35)
## prs_scaled:age.firstbirth.group[35,80)
## prs_scaled:age.firstbirth.group[80,1e+03)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 7028.9 on 38488 degrees of freedom
## Residual deviance: 6755.9 on 38428 degrees of freedom
## AIC: 6877.9
##
## Number of Fisher Scoring iterations: 15
fit.int.all3.premeno <- glm(breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+factor(oc.cate3)+BMI.scale+relevel(factor(dat_test_complete$assessment_center),ref = "11001")+alcohol+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:factor(oc.cate3)+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group, data=dat_test_complete,family = binomial(), model = FALSE, x = FALSE, y = FALSE)
summary(fit.int.all3.premeno)
##
## Call:
## glm(formula = breast_cancer ~ prs_scaled + PC1 + PC2 + PC3 +
## PC4 + PC5 + PC6 + PC7 + PC8 + PC9 + PC10 + agegroups + n.children.scale +
## birth.x + birth.y + age.firstbirth.group + height.scale +
## age.menarche.scale + factor(oc.cate3) + BMI.scale + relevel(factor(dat_test_complete$assessment_center),
## ref = "11001") + alcohol + prs_scaled:birth.x + prs_scaled:birth.y +
## prs_scaled:factor(oc.cate3) + prs_scaled:age.menarche.scale +
## prs_scaled:BMI.scale + prs_scaled:agegroups + prs_scaled:alcohol +
## prs_scaled:height.scale + prs_scaled:n.children.scale + prs_scaled:age.firstbirth.group,
## family = binomial(), data = dat_test_complete, model = FALSE,
## x = FALSE, y = FALSE)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.7927 -0.2146 -0.1758 -0.1389 3.4537
##
## Coefficients:
## Estimate
## (Intercept) -4.901e+00
## prs_scaled 4.356e-01
## PC1 -2.401e-02
## PC2 -1.936e-02
## PC3 1.233e-02
## PC4 -8.849e-03
## PC5 -1.193e-03
## PC6 4.850e-02
## PC7 1.888e-02
## PC8 -2.522e-02
## PC9 9.153e-04
## PC10 8.395e-03
## agegroups[45,50) 2.043e-01
## agegroups[50,80) 1.691e-01
## n.children.scale 1.278e-01
## birth.x 7.774e-03
## birth.y 8.091e-02
## age.firstbirth.group[25,35) 2.962e-01
## age.firstbirth.group[35,80) 4.888e-01
## age.firstbirth.group[80,1e+03) 6.526e-01
## height.scale 1.052e-01
## age.menarche.scale -7.545e-03
## factor(oc.cate3)1 -3.521e-01
## factor(oc.cate3)2 -2.592e-01
## factor(oc.cate3)3 -5.787e-02
## factor(oc.cate3)4 1.117e-01
## BMI.scale 1.831e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 4.746e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 1.750e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 3.354e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 1.257e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 8.096e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 4.124e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 2.527e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 3.894e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 1.383e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 1.200e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -7.624e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -5.221e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -7.514e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -2.779e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -2.437e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -1.911e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -2.659e-03
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -3.363e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -4.039e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -1.236e+01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -1.226e+01
## alcohol 1.894e-01
## prs_scaled:birth.x -1.554e-02
## prs_scaled:birth.y -2.253e-03
## prs_scaled:factor(oc.cate3)1 1.455e-01
## prs_scaled:factor(oc.cate3)2 3.554e-02
## prs_scaled:factor(oc.cate3)3 -6.933e-02
## prs_scaled:factor(oc.cate3)4 -6.159e-02
## prs_scaled:age.menarche.scale -3.071e-02
## prs_scaled:BMI.scale -2.831e-02
## prs_scaled:agegroups[45,50) 2.475e-02
## prs_scaled:agegroups[50,80) 1.410e-01
## prs_scaled:alcohol 5.203e-02
## prs_scaled:height.scale 1.157e-03
## prs_scaled:n.children.scale 2.669e-04
## prs_scaled:age.firstbirth.group[25,35) -3.195e-02
## prs_scaled:age.firstbirth.group[35,80) 3.460e-02
## prs_scaled:age.firstbirth.group[80,1e+03) -4.382e-02
## Std. Error
## (Intercept) 3.457e-01
## prs_scaled 1.940e-01
## PC1 1.667e-02
## PC2 1.444e-02
## PC3 1.670e-02
## PC4 8.738e-03
## PC5 6.356e-03
## PC6 2.132e-02
## PC7 1.037e-02
## PC8 1.437e-02
## PC9 1.021e-02
## PC10 1.745e-02
## agegroups[45,50) 9.566e-02
## agegroups[50,80) 1.196e-01
## n.children.scale 7.603e-02
## birth.x 5.729e-02
## birth.y 6.552e-02
## age.firstbirth.group[25,35) 1.291e-01
## age.firstbirth.group[35,80) 1.842e-01
## age.firstbirth.group[80,1e+03) 2.130e-01
## height.scale 4.361e-02
## age.menarche.scale 4.317e-02
## factor(oc.cate3)1 1.849e-01
## factor(oc.cate3)2 1.738e-01
## factor(oc.cate3)3 1.663e-01
## factor(oc.cate3)4 1.526e-01
## BMI.scale 4.370e-02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 1.041e+00
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 3.018e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 2.944e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 2.988e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 2.933e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 2.808e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 2.666e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 2.661e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 2.662e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 2.527e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 2.626e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 3.932e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 2.712e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 2.883e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 2.857e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 3.087e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 2.858e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 3.122e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 3.177e-01
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 1.935e+02
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 3.404e+02
## alcohol 1.240e-01
## prs_scaled:birth.x 4.388e-02
## prs_scaled:birth.y 4.237e-02
## prs_scaled:factor(oc.cate3)1 1.632e-01
## prs_scaled:factor(oc.cate3)2 1.560e-01
## prs_scaled:factor(oc.cate3)3 1.515e-01
## prs_scaled:factor(oc.cate3)4 1.392e-01
## prs_scaled:age.menarche.scale 3.989e-02
## prs_scaled:BMI.scale 4.067e-02
## prs_scaled:agegroups[45,50) 8.769e-02
## prs_scaled:agegroups[50,80) 1.068e-01
## prs_scaled:alcohol 1.147e-01
## prs_scaled:height.scale 3.896e-02
## prs_scaled:n.children.scale 6.784e-02
## prs_scaled:age.firstbirth.group[25,35) 1.157e-01
## prs_scaled:age.firstbirth.group[35,80) 1.659e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 1.911e-01
## z value
## (Intercept) -14.179
## prs_scaled 2.245
## PC1 -1.440
## PC2 -1.341
## PC3 0.738
## PC4 -1.013
## PC5 -0.188
## PC6 2.275
## PC7 1.820
## PC8 -1.755
## PC9 0.090
## PC10 0.481
## agegroups[45,50) 2.136
## agegroups[50,80) 1.414
## n.children.scale 1.681
## birth.x 0.136
## birth.y 1.235
## age.firstbirth.group[25,35) 2.294
## age.firstbirth.group[35,80) 2.654
## age.firstbirth.group[80,1e+03) 3.063
## height.scale 2.412
## age.menarche.scale -0.175
## factor(oc.cate3)1 -1.904
## factor(oc.cate3)2 -1.492
## factor(oc.cate3)3 -0.348
## factor(oc.cate3)4 0.732
## BMI.scale 0.419
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.456
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.580
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 1.139
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.421
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.276
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 1.469
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.948
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 1.463
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.519
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.475
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 -0.290
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 -1.328
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 -0.277
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 -0.964
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 -0.853
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 -0.619
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 -0.009
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 -1.077
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 -1.271
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 -0.064
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 -0.036
## alcohol 1.527
## prs_scaled:birth.x -0.354
## prs_scaled:birth.y -0.053
## prs_scaled:factor(oc.cate3)1 0.891
## prs_scaled:factor(oc.cate3)2 0.228
## prs_scaled:factor(oc.cate3)3 -0.458
## prs_scaled:factor(oc.cate3)4 -0.443
## prs_scaled:age.menarche.scale -0.770
## prs_scaled:BMI.scale -0.696
## prs_scaled:agegroups[45,50) 0.282
## prs_scaled:agegroups[50,80) 1.320
## prs_scaled:alcohol 0.454
## prs_scaled:height.scale 0.030
## prs_scaled:n.children.scale 0.004
## prs_scaled:age.firstbirth.group[25,35) -0.276
## prs_scaled:age.firstbirth.group[35,80) 0.209
## prs_scaled:age.firstbirth.group[80,1e+03) -0.229
## Pr(>|z|)
## (Intercept) < 2e-16
## prs_scaled 0.02474
## PC1 0.14977
## PC2 0.17997
## PC3 0.46036
## PC4 0.31118
## PC5 0.85112
## PC6 0.02288
## PC7 0.06883
## PC8 0.07919
## PC9 0.92855
## PC10 0.63055
## agegroups[45,50) 0.03270
## agegroups[50,80) 0.15733
## n.children.scale 0.09271
## birth.x 0.89206
## birth.y 0.21683
## age.firstbirth.group[25,35) 0.02181
## age.firstbirth.group[35,80) 0.00796
## age.firstbirth.group[80,1e+03) 0.00219
## height.scale 0.01587
## age.menarche.scale 0.86124
## factor(oc.cate3)1 0.05689
## factor(oc.cate3)2 0.13574
## factor(oc.cate3)3 0.72793
## factor(oc.cate3)4 0.46435
## BMI.scale 0.67513
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003 0.64851
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002 0.56198
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003 0.25459
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004 0.67407
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005 0.78250
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006 0.14191
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007 0.34330
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008 0.14343
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009 0.60347
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010 0.63492
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011 0.77157
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012 0.18418
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013 0.78177
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014 0.33509
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016 0.39367
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017 0.53603
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018 0.99258
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020 0.28141
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021 0.20357
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022 0.94906
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023 0.97127
## alcohol 0.12678
## prs_scaled:birth.x 0.72315
## prs_scaled:birth.y 0.95759
## prs_scaled:factor(oc.cate3)1 0.37274
## prs_scaled:factor(oc.cate3)2 0.81972
## prs_scaled:factor(oc.cate3)3 0.64724
## prs_scaled:factor(oc.cate3)4 0.65812
## prs_scaled:age.menarche.scale 0.44135
## prs_scaled:BMI.scale 0.48640
## prs_scaled:agegroups[45,50) 0.77778
## prs_scaled:agegroups[50,80) 0.18695
## prs_scaled:alcohol 0.65002
## prs_scaled:height.scale 0.97631
## prs_scaled:n.children.scale 0.99686
## prs_scaled:age.firstbirth.group[25,35) 0.78251
## prs_scaled:age.firstbirth.group[35,80) 0.83482
## prs_scaled:age.firstbirth.group[80,1e+03) 0.81862
##
## (Intercept) ***
## prs_scaled *
## PC1
## PC2
## PC3
## PC4
## PC5
## PC6 *
## PC7 .
## PC8 .
## PC9
## PC10
## agegroups[45,50) *
## agegroups[50,80)
## n.children.scale .
## birth.x
## birth.y
## age.firstbirth.group[25,35) *
## age.firstbirth.group[35,80) **
## age.firstbirth.group[80,1e+03) **
## height.scale *
## age.menarche.scale
## factor(oc.cate3)1 .
## factor(oc.cate3)2
## factor(oc.cate3)3
## factor(oc.cate3)4
## BMI.scale
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")10003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11002
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11003
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11004
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11005
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11006
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11007
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11008
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11009
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11010
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11011
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11012
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11013
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11014
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11016
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11017
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11018
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11020
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11021
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11022
## relevel(factor(dat_test_complete$assessment_center), ref = "11001")11023
## alcohol
## prs_scaled:birth.x
## prs_scaled:birth.y
## prs_scaled:factor(oc.cate3)1
## prs_scaled:factor(oc.cate3)2
## prs_scaled:factor(oc.cate3)3
## prs_scaled:factor(oc.cate3)4
## prs_scaled:age.menarche.scale
## prs_scaled:BMI.scale
## prs_scaled:agegroups[45,50)
## prs_scaled:agegroups[50,80)
## prs_scaled:alcohol
## prs_scaled:height.scale
## prs_scaled:n.children.scale
## prs_scaled:age.firstbirth.group[25,35)
## prs_scaled:age.firstbirth.group[35,80)
## prs_scaled:age.firstbirth.group[80,1e+03)
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 7028.9 on 38488 degrees of freedom
## Residual deviance: 6752.5 on 38424 degrees of freedom
## AIC: 6882.5
##
## Number of Fisher Scoring iterations: 15
#Now let's select the control samples for the case/control study
table(dat_test_complete$breast_cancer)
##
## 0 1
## 37785 704
#select 704 controls who did not have breast cancer
control=dat_test_complete[which(dat_test_complete$breast_cancer==0),]
set.seed(10252022)
control=control[sample(1:dim(control)[1],size=704,replace = F),]
dat_test_casecontrol=rbind(control,dat_test_complete[which(dat_test_complete$breast_cancer==1),])
dat_test_casecontrol$prs_scaled=scale(dat_test_casecontrol$prs_bc,center = T,scale = T)
dat_test_casecontrol$age.menarche.scale=scale(dat_test_casecontrol$age.menarche,center = T,scale=T)
dat_test_casecontrol$n.children.scale=scale(dat_test_casecontrol$n.children.win,center=T,scale = T)
dat_test_casecontrol$height.scale=scale(dat_test_casecontrol$height,center=T,scale = T)
dat_test_casecontrol$BMI.scale=scale(dat_test_casecontrol$BMI,center=T,scale = T)
dat_test_casecontrol$length.oc.scale=scale(dat_test_casecontrol$length.oc,center=T,scale = T)
dat_test_casecontrol$birth.x=scale(dat_test_casecontrol$birth.x,center=T,scale=T)
dat_test_casecontrol$birth.y=scale(dat_test_casecontrol$birth.y,center=T,scale=T)
dat_test_casecontrol.coordinate=dat_test_casecontrol[complete.cases(dat_test_casecontrol),]
table(dat_test_casecontrol.coordinate$breast_cancer)
##
## 0 1
## 704 704
dat_test_casecontrol.coordinate$assessment_center=factor(dat_test_casecontrol.coordinate$assessment_center)
dat_test_casecontrol.coordinate$assessment_center=relevel(dat_test_casecontrol.coordinate$assessment_center,ref = "11001")
fit_normal.coordinate1.premeno<-prs_e_function_gr(data=dat_test_casecontrol.coordinate,
formula = breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+length.oc.scale+BMI.scale+assessment_center+alcohol+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:length.oc.scale+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group,
formula_prs = prs_scaled ~ PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+birth.x+birth.y,
numDeriv = F,
facVar="assessment_center")
## After removing missing values, the number of observations is 1408
## initial value 2899.717713
## iter 50 value 2878.712959
## final value 2878.045107
## converged
fit_normal.coordinate2.premeno<-prs_e_function_gr(data=dat_test_casecontrol.coordinate,
formula = breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+factor(oc.cate2)+BMI.scale+assessment_center+alcohol+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:factor(oc.cate2)+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group,
formula_prs = prs_scaled ~ PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+birth.x+birth.y,
numDeriv = F,
facVar="assessment_center")
## After removing missing values, the number of observations is 1408
## initial value 2894.601813
## iter 50 value 2874.418008
## final value 2873.837624
## converged
fit_normal.coordinate3.premeno<-prs_e_function_gr(data=dat_test_casecontrol.coordinate,
formula = breast_cancer~prs_scaled+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+factor(oc.cate3)+BMI.scale+assessment_center+alcohol+prs_scaled:birth.x+prs_scaled:birth.y+prs_scaled:factor(oc.cate3)+prs_scaled:age.menarche.scale+prs_scaled:BMI.scale+prs_scaled:agegroups+prs_scaled:alcohol+prs_scaled:height.scale+prs_scaled:n.children.scale+prs_scaled:age.firstbirth.group,
formula_prs = prs_scaled ~ PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+birth.x+birth.y,
numDeriv = F,
facVar="assessment_center")
## After removing missing values, the number of observations is 1408
## initial value 2894.543856
## iter 50 value 2873.815226
## final value 2873.572471
## converged
#Print the results, our method
fit_normal.coordinate1.premeno$res_normal
## Estimate Std.Error
## (Intercept) -8.269280e-01 4.548883e-01
## prs_scaled 4.542047e-01 1.643696e-01
## PC1 -2.558438e-02 2.337236e-02
## PC2 -3.497893e-02 2.472434e-02
## PC3 3.868873e-02 3.117105e-02
## PC4 3.593217e-03 1.488781e-02
## PC5 -6.884867e-03 9.344226e-03
## PC6 7.026714e-02 3.320704e-02
## PC7 2.372458e-02 1.486668e-02
## PC8 -6.034577e-02 2.168831e-02
## PC9 -5.854040e-04 1.490000e-02
## PC10 -1.916557e-02 2.733881e-02
## agegroups[45,50) 3.650722e-01 1.279668e-01
## agegroups[50,80) 2.512753e-01 1.563238e-01
## n.children.scale 1.659684e-01 9.927062e-02
## birth.x 4.640277e-02 7.894811e-02
## birth.y 7.096295e-02 9.151537e-02
## age.firstbirth.group[25,35) 2.139111e-01 1.661355e-01
## age.firstbirth.group[35,80) 5.417790e-01 2.440843e-01
## age.firstbirth.group[80,1e+03) 7.564740e-01 2.753546e-01
## height.scale 7.987473e-02 5.798382e-02
## age.menarche.scale -2.861460e-02 5.713823e-02
## length.oc.scale 8.492363e-02 5.688934e-02
## BMI.scale 3.903553e-02 5.799412e-02
## assessment_center10003 1.441584e+01 1.352772e+03
## assessment_center11002 2.762022e-01 4.439040e-01
## assessment_center11003 6.663534e-01 4.425624e-01
## assessment_center11004 1.931194e-01 4.329954e-01
## assessment_center11005 2.284277e-01 4.265564e-01
## assessment_center11006 3.620310e-01 4.064697e-01
## assessment_center11007 7.423235e-02 3.766943e-01
## assessment_center11008 4.369356e-01 3.874189e-01
## assessment_center11009 2.817981e-01 3.832897e-01
## assessment_center11010 2.873712e-01 3.597294e-01
## assessment_center11011 -1.102428e-01 3.684821e-01
## assessment_center11012 -2.096053e-01 5.393307e-01
## assessment_center11013 2.920107e-01 3.939899e-01
## assessment_center11014 -4.601950e-02 4.034813e-01
## assessment_center11016 -1.471340e-01 3.947241e-01
## assessment_center11017 -5.930094e-01 4.151474e-01
## assessment_center11018 -3.005023e-01 3.936160e-01
## assessment_center11020 -4.564929e-01 4.277204e-01
## assessment_center11021 -1.673695e-01 4.432721e-01
## assessment_center11022 -1.422272e+01 9.086527e+02
## alcohol 6.824005e-02 1.626758e-01
## prs_scaled:birth.x -2.105416e-02 6.339035e-02
## prs_scaled:birth.y 2.619643e-03 6.339225e-02
## prs_scaled:length.oc.scale -8.362498e-02 3.937142e-02
## prs_scaled:age.menarche.scale -2.531219e-02 3.989727e-02
## prs_scaled:BMI.scale -3.248636e-02 4.006528e-02
## prs_scaled:agegroups[45,50) 1.312336e-02 9.055365e-02
## prs_scaled:agegroups[50,80) 1.255340e-01 1.102676e-01
## prs_scaled:alcohol 6.945791e-02 1.175117e-01
## prs_scaled:height.scale -3.642083e-03 4.049962e-02
## prs_scaled:n.children.scale 1.477038e-02 6.959438e-02
## prs_scaled:age.firstbirth.group[25,35) -1.384160e-02 1.192467e-01
## prs_scaled:age.firstbirth.group[35,80) 3.971260e-02 1.675649e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -4.538395e-04 1.945985e-01
## eta_(Intercept) -3.004578e-01 8.305741e-02
## eta_PC1 -5.776163e-03 6.700804e-03
## eta_PC2 -2.485202e-04 9.122994e-03
## eta_PC3 1.252684e-02 1.398803e-02
## eta_PC4 4.413829e-03 6.446549e-03
## eta_PC5 -2.709303e-03 4.093081e-03
## eta_PC6 1.867398e-04 1.513566e-02
## eta_PC7 8.294567e-03 6.598633e-03
## eta_PC8 -1.849780e-03 9.833610e-03
## eta_PC9 -2.806268e-04 6.529570e-03
## eta_PC10 -2.395467e-03 1.244716e-02
## eta_birth.x 9.475703e-03 4.175363e-02
## eta_birth.y 5.874407e-03 4.462461e-02
## sigma_stratadata[, facVar]11001 9.141192e-01 8.819766e-02
## sigma_stratadata[, facVar]10003 2.637547e-01 2.220114e-01
## sigma_stratadata[, facVar]11002 9.441194e-01 8.808938e-02
## sigma_stratadata[, facVar]11003 9.664791e-01 8.125759e-02
## sigma_stratadata[, facVar]11004 9.690319e-01 7.436885e-02
## sigma_stratadata[, facVar]11005 9.443220e-01 7.650728e-02
## sigma_stratadata[, facVar]11006 9.716573e-01 7.581669e-02
## sigma_stratadata[, facVar]11007 9.212861e-01 5.786060e-02
## sigma_stratadata[, facVar]11008 9.369924e-01 6.475685e-02
## sigma_stratadata[, facVar]11009 9.963599e-01 6.160843e-02
## sigma_stratadata[, facVar]11010 1.019698e+00 5.506250e-02
## sigma_stratadata[, facVar]11011 9.427020e-01 5.211507e-02
## sigma_stratadata[, facVar]11012 8.908023e-01 1.199856e-01
## sigma_stratadata[, facVar]11013 9.037637e-01 6.493505e-02
## sigma_stratadata[, facVar]11014 9.119175e-01 7.337680e-02
## sigma_stratadata[, facVar]11016 9.336310e-01 6.868496e-02
## sigma_stratadata[, facVar]11017 1.067494e+00 8.366302e-02
## sigma_stratadata[, facVar]11018 9.228904e-01 6.712057e-02
## sigma_stratadata[, facVar]11020 1.102430e+00 9.268883e-02
## sigma_stratadata[, facVar]11021 9.289243e-01 8.983780e-02
## sigma_stratadata[, facVar]11022 7.065314e-01 2.934857e-01
## Z.value Pvalue
## (Intercept) -1.817870486 6.908393e-02
## prs_scaled 2.763313844 5.721772e-03
## PC1 -1.094642608 2.736732e-01
## PC2 -1.414756875 1.571398e-01
## PC3 1.241174944 2.145411e-01
## PC4 0.241352985 8.092815e-01
## PC5 -0.736804474 4.612413e-01
## PC6 2.116031655 3.434212e-02
## PC7 1.595822378 1.105285e-01
## PC8 -2.782409863 5.395685e-03
## PC9 -0.039288867 9.686601e-01
## PC10 -0.701039002 4.832787e-01
## agegroups[45,50) 2.852866135 4.332687e-03
## agegroups[50,80) 1.607402828 1.079660e-01
## n.children.scale 1.671878698 9.454824e-02
## birth.x 0.587762851 5.566915e-01
## birth.y 0.775421188 4.380908e-01
## age.firstbirth.group[25,35) 1.287570362 1.978956e-01
## age.firstbirth.group[35,80) 2.219638954 2.644329e-02
## age.firstbirth.group[80,1e+03) 2.747272220 6.009323e-03
## height.scale 1.377534880 1.683469e-01
## age.menarche.scale -0.500796036 6.165147e-01
## length.oc.scale 1.492786188 1.354932e-01
## BMI.scale 0.673094531 5.008872e-01
## assessment_center10003 0.010656519 9.914975e-01
## assessment_center11002 0.622211686 5.338027e-01
## assessment_center11003 1.505671131 1.321516e-01
## assessment_center11004 0.446008089 6.555914e-01
## assessment_center11005 0.535515792 5.922932e-01
## assessment_center11006 0.890671464 3.731054e-01
## assessment_center11007 0.197062611 8.437785e-01
## assessment_center11008 1.127811799 2.593994e-01
## assessment_center11009 0.735209040 4.622122e-01
## assessment_center11010 0.798853622 4.243753e-01
## assessment_center11011 -0.299180789 7.648021e-01
## assessment_center11012 -0.388639665 6.975427e-01
## assessment_center11013 0.741162997 4.585946e-01
## assessment_center11014 -0.114056078 9.091933e-01
## assessment_center11016 -0.372751393 7.093335e-01
## assessment_center11017 -1.428430913 1.531679e-01
## assessment_center11018 -0.763440347 4.452008e-01
## assessment_center11020 -1.067269215 2.858503e-01
## assessment_center11021 -0.377577432 7.057445e-01
## assessment_center11022 -0.015652542 9.875116e-01
## alcohol 0.419485079 6.748617e-01
## prs_scaled:birth.x -0.332135164 7.397872e-01
## prs_scaled:birth.y 0.041324345 9.670373e-01
## prs_scaled:length.oc.scale -2.124002227 3.366996e-02
## prs_scaled:age.menarche.scale -0.634434023 5.257976e-01
## prs_scaled:BMI.scale -0.810835659 4.174601e-01
## prs_scaled:agegroups[45,50) 0.144923592 8.847712e-01
## prs_scaled:agegroups[50,80) 1.138448788 2.549331e-01
## prs_scaled:alcohol 0.591072523 5.544718e-01
## prs_scaled:height.scale -0.089928815 9.283438e-01
## prs_scaled:n.children.scale 0.212235311 8.319235e-01
## prs_scaled:age.firstbirth.group[25,35) -0.116075354 9.075928e-01
## prs_scaled:age.firstbirth.group[35,80) 0.236998288 8.126581e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -0.002332185 9.981392e-01
## eta_(Intercept) -3.617471400 2.974952e-04
## eta_PC1 -0.862010475 3.886818e-01
## eta_PC2 -0.027241079 9.782675e-01
## eta_PC3 0.895539673 3.704987e-01
## eta_PC4 0.684680928 4.935453e-01
## eta_PC5 -0.661922666 5.080208e-01
## eta_PC6 0.012337738 9.901562e-01
## eta_PC7 1.257012795 2.087490e-01
## eta_PC8 -0.188107959 8.507920e-01
## eta_PC9 -0.042977832 9.657192e-01
## eta_PC10 -0.192450887 8.473890e-01
## eta_birth.x 0.226943181 8.204679e-01
## eta_birth.y 0.131640528 8.952686e-01
## sigma_stratadata[, facVar]11001 10.364439263 3.598629e-25
## sigma_stratadata[, facVar]10003 1.188023491 2.348242e-01
## sigma_stratadata[, facVar]11002 10.717743000 8.402879e-27
## sigma_stratadata[, facVar]11003 11.894016844 1.271414e-32
## sigma_stratadata[, facVar]11004 13.030077787 8.252348e-39
## sigma_stratadata[, facVar]11005 12.342904383 5.320151e-35
## sigma_stratadata[, facVar]11006 12.815875585 1.336214e-37
## sigma_stratadata[, facVar]11007 15.922511357 4.422631e-57
## sigma_stratadata[, facVar]11008 14.469394649 1.891293e-47
## sigma_stratadata[, facVar]11009 16.172459645 7.888503e-59
## sigma_stratadata[, facVar]11010 18.518927572 1.453026e-76
## sigma_stratadata[, facVar]11011 18.088857310 3.900917e-73
## sigma_stratadata[, facVar]11012 7.424240538 1.134289e-13
## sigma_stratadata[, facVar]11013 13.917965628 4.927300e-44
## sigma_stratadata[, facVar]11014 12.427873099 1.844775e-35
## sigma_stratadata[, facVar]11016 13.592946163 4.409662e-42
## sigma_stratadata[, facVar]11017 12.759449732 2.761449e-37
## sigma_stratadata[, facVar]11018 13.749741846 5.111158e-43
## sigma_stratadata[, facVar]11020 11.893881613 1.273475e-32
## sigma_stratadata[, facVar]11021 10.340016746 4.644564e-25
## sigma_stratadata[, facVar]11022 2.407379188 1.606748e-02
fit_normal.coordinate2.premeno$res_normal
## Estimate Std.Error
## (Intercept) -6.036384e-01 4.914734e-01
## prs_scaled 4.856305e-01 1.998392e-01
## PC1 -2.407773e-02 2.353074e-02
## PC2 -3.241733e-02 2.492873e-02
## PC3 3.938896e-02 3.128143e-02
## PC4 3.331982e-03 1.490957e-02
## PC5 -7.741436e-03 9.369597e-03
## PC6 7.547927e-02 3.330043e-02
## PC7 2.436134e-02 1.491927e-02
## PC8 -6.102503e-02 2.175224e-02
## PC9 -3.905199e-04 1.494606e-02
## PC10 -1.863641e-02 2.740757e-02
## agegroups[45,50) 3.777763e-01 1.284823e-01
## agegroups[50,80) 2.688612e-01 1.570744e-01
## n.children.scale 1.730633e-01 9.964890e-02
## birth.x 5.125000e-02 7.936395e-02
## birth.y 6.901322e-02 9.190932e-02
## age.firstbirth.group[25,35) 2.270733e-01 1.668931e-01
## age.firstbirth.group[35,80) 5.221605e-01 2.448607e-01
## age.firstbirth.group[80,1e+03) 7.400388e-01 2.768563e-01
## height.scale 8.036553e-02 5.819322e-02
## age.menarche.scale -2.862161e-02 5.736327e-02
## factor(oc.cate2)1 -5.119388e-01 2.173620e-01
## factor(oc.cate2)2 -1.073318e-01 2.083972e-01
## BMI.scale 3.870995e-02 5.825690e-02
## assessment_center10003 1.431803e+01 1.357102e+03
## assessment_center11002 2.790522e-01 4.449475e-01
## assessment_center11003 6.568132e-01 4.443218e-01
## assessment_center11004 1.897913e-01 4.342305e-01
## assessment_center11005 2.568709e-01 4.275473e-01
## assessment_center11006 3.929606e-01 4.075374e-01
## assessment_center11007 6.610801e-02 3.774580e-01
## assessment_center11008 4.502624e-01 3.883943e-01
## assessment_center11009 2.901477e-01 3.844263e-01
## assessment_center11010 2.695464e-01 3.605206e-01
## assessment_center11011 -1.168405e-01 3.693260e-01
## assessment_center11012 -1.437975e-01 5.407695e-01
## assessment_center11013 3.211362e-01 3.946652e-01
## assessment_center11014 -5.541862e-02 4.045419e-01
## assessment_center11016 -1.583712e-01 3.959833e-01
## assessment_center11017 -6.047008e-01 4.161103e-01
## assessment_center11018 -3.104998e-01 3.948133e-01
## assessment_center11020 -4.372980e-01 4.284127e-01
## assessment_center11021 -1.723390e-01 4.438873e-01
## assessment_center11022 -1.423605e+01 9.052690e+02
## alcohol 8.157501e-02 1.637920e-01
## prs_scaled:birth.x -2.389570e-02 6.339617e-02
## prs_scaled:birth.y 2.118811e-03 6.342680e-02
## prs_scaled:factor(oc.cate2)1 8.230418e-02 1.461940e-01
## prs_scaled:factor(oc.cate2)2 -8.838775e-02 1.375803e-01
## prs_scaled:age.menarche.scale -2.597528e-02 3.996804e-02
## prs_scaled:BMI.scale -3.216953e-02 3.995744e-02
## prs_scaled:agegroups[45,50) 7.384435e-03 9.059493e-02
## prs_scaled:agegroups[50,80) 1.244129e-01 1.103879e-01
## prs_scaled:alcohol 6.263881e-02 1.177404e-01
## prs_scaled:height.scale -4.243693e-03 4.059175e-02
## prs_scaled:n.children.scale 1.738340e-02 6.947587e-02
## prs_scaled:age.firstbirth.group[25,35) -1.383778e-02 1.191315e-01
## prs_scaled:age.firstbirth.group[35,80) 4.447126e-02 1.673987e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 7.086129e-03 1.944932e-01
## eta_(Intercept) -3.007873e-01 8.303537e-02
## eta_PC1 -5.842309e-03 6.695367e-03
## eta_PC2 -4.624998e-04 9.122451e-03
## eta_PC3 1.238988e-02 1.399815e-02
## eta_PC4 4.485884e-03 6.449913e-03
## eta_PC5 -2.434971e-03 4.095762e-03
## eta_PC6 -6.673611e-04 1.514684e-02
## eta_PC7 8.078356e-03 6.600803e-03
## eta_PC8 -1.587794e-03 9.836592e-03
## eta_PC9 -4.143236e-04 6.531120e-03
## eta_PC10 -1.905985e-03 1.246241e-02
## eta_birth.x 1.041036e-02 4.174553e-02
## eta_birth.y 5.927429e-03 4.469251e-02
## sigma_stratadata[, facVar]11001 9.149430e-01 8.837144e-02
## sigma_stratadata[, facVar]10003 2.620924e-01 2.214623e-01
## sigma_stratadata[, facVar]11002 9.440187e-01 8.807499e-02
## sigma_stratadata[, facVar]11003 9.679840e-01 8.163155e-02
## sigma_stratadata[, facVar]11004 9.698911e-01 7.458851e-02
## sigma_stratadata[, facVar]11005 9.424026e-01 7.620024e-02
## sigma_stratadata[, facVar]11006 9.716158e-01 7.576074e-02
## sigma_stratadata[, facVar]11007 9.213945e-01 5.789866e-02
## sigma_stratadata[, facVar]11008 9.372689e-01 6.471986e-02
## sigma_stratadata[, facVar]11009 9.974989e-01 6.174909e-02
## sigma_stratadata[, facVar]11010 1.020470e+00 5.520308e-02
## sigma_stratadata[, facVar]11011 9.429172e-01 5.213514e-02
## sigma_stratadata[, facVar]11012 8.891882e-01 1.191879e-01
## sigma_stratadata[, facVar]11013 9.015366e-01 6.453782e-02
## sigma_stratadata[, facVar]11014 9.127298e-01 7.350067e-02
## sigma_stratadata[, facVar]11016 9.363416e-01 6.920795e-02
## sigma_stratadata[, facVar]11017 1.067561e+00 8.364555e-02
## sigma_stratadata[, facVar]11018 9.233604e-01 6.725673e-02
## sigma_stratadata[, facVar]11020 1.102178e+00 9.265633e-02
## sigma_stratadata[, facVar]11021 9.274174e-01 8.950612e-02
## sigma_stratadata[, facVar]11022 7.088441e-01 2.946511e-01
## Z.value Pvalue
## (Intercept) -1.22822177 2.193637e-01
## prs_scaled 2.43010630 1.509440e-02
## PC1 -1.02324566 3.061917e-01
## PC2 -1.30040025 1.934638e-01
## PC3 1.25918044 2.079652e-01
## PC4 0.22347934 8.231625e-01
## PC5 -0.82622931 4.086740e-01
## PC6 2.26661554 2.341372e-02
## PC7 1.63287752 1.024948e-01
## PC8 -2.80545906 5.024496e-03
## PC9 -0.02612863 9.791547e-01
## PC10 -0.67997313 4.965215e-01
## agegroups[45,50) 2.94029784 3.278969e-03
## agegroups[50,80) 1.71168024 8.695561e-02
## n.children.scale 1.73673083 8.243469e-02
## birth.x 0.64575924 5.184353e-01
## birth.y 0.75088377 4.527226e-01
## age.firstbirth.group[25,35) 1.36059139 1.736429e-01
## age.firstbirth.group[35,80) 2.13247967 3.296743e-02
## age.firstbirth.group[80,1e+03) 2.67300734 7.517461e-03
## height.scale 1.38101190 1.672753e-01
## age.menarche.scale -0.49895368 6.178120e-01
## factor(oc.cate2)1 -2.35523555 1.851097e-02
## factor(oc.cate2)2 -0.51503466 6.065288e-01
## BMI.scale 0.66446988 5.063896e-01
## assessment_center10003 0.01055045 9.915821e-01
## assessment_center11002 0.62715755 5.305560e-01
## assessment_center11003 1.47823769 1.393442e-01
## assessment_center11004 0.43707505 6.620569e-01
## assessment_center11005 0.60080109 5.479725e-01
## assessment_center11006 0.96423210 3.349296e-01
## assessment_center11007 0.17514005 8.609696e-01
## assessment_center11008 1.15929179 2.463373e-01
## assessment_center11009 0.75475509 4.503959e-01
## assessment_center11010 0.74765884 4.546660e-01
## assessment_center11011 -0.31636141 7.517282e-01
## assessment_center11012 -0.26591279 7.903064e-01
## assessment_center11013 0.81369287 4.158209e-01
## assessment_center11014 -0.13699105 8.910379e-01
## assessment_center11016 -0.39994430 6.891975e-01
## assessment_center11017 -1.45322260 1.461620e-01
## assessment_center11018 -0.78644719 4.316055e-01
## assessment_center11020 -1.02074003 3.073776e-01
## assessment_center11021 -0.38824937 6.978315e-01
## assessment_center11022 -0.01572577 9.874532e-01
## alcohol 0.49804039 6.184556e-01
## prs_scaled:birth.x -0.37692654 7.062282e-01
## prs_scaled:birth.y 0.03340561 9.733511e-01
## prs_scaled:factor(oc.cate2)1 0.56297918 5.734491e-01
## prs_scaled:factor(oc.cate2)2 -0.64244459 5.205846e-01
## prs_scaled:age.menarche.scale -0.64990122 5.157560e-01
## prs_scaled:BMI.scale -0.80509478 4.207650e-01
## prs_scaled:agegroups[45,50) 0.08151047 9.350360e-01
## prs_scaled:agegroups[50,80) 1.12705180 2.597206e-01
## prs_scaled:alcohol 0.53200793 5.947205e-01
## prs_scaled:height.scale -0.10454570 9.167363e-01
## prs_scaled:n.children.scale 0.25020778 8.024267e-01
## prs_scaled:age.firstbirth.group[25,35) -0.11615555 9.075293e-01
## prs_scaled:age.firstbirth.group[35,80) 0.26566075 7.905005e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 0.03643382 9.709364e-01
## eta_(Intercept) -3.62239978 2.918826e-04
## eta_PC1 -0.87258972 3.828867e-01
## eta_PC2 -0.05069907 9.595653e-01
## eta_PC3 0.88510869 3.760980e-01
## eta_PC4 0.69549527 4.867450e-01
## eta_PC5 -0.59450982 5.521712e-01
## eta_PC6 -0.04405943 9.648570e-01
## eta_PC7 1.22384444 2.210109e-01
## eta_PC8 -0.16141705 8.717649e-01
## eta_PC9 -0.06343836 9.494174e-01
## eta_PC10 -0.15293876 8.784466e-01
## eta_birth.x 0.24937664 8.030695e-01
## eta_birth.y 0.13262689 8.944885e-01
## sigma_stratadata[, facVar]11001 10.35337928 4.039702e-25
## sigma_stratadata[, facVar]10003 1.18346318 2.366256e-01
## sigma_stratadata[, facVar]11002 10.71835169 8.347771e-27
## sigma_stratadata[, facVar]11003 11.85796386 1.956758e-32
## sigma_stratadata[, facVar]11004 13.00322402 1.172922e-38
## sigma_stratadata[, facVar]11005 12.36744921 3.920757e-35
## sigma_stratadata[, facVar]11006 12.82479196 1.191058e-37
## sigma_stratadata[, facVar]11007 15.91391544 5.073862e-57
## sigma_stratadata[, facVar]11008 14.48193718 1.575923e-47
## sigma_stratadata[, facVar]11009 16.15406669 1.063155e-58
## sigma_stratadata[, facVar]11010 18.48575037 2.689316e-76
## sigma_stratadata[, facVar]11011 18.08601837 4.107099e-73
## sigma_stratadata[, facVar]11012 7.46038757 8.626834e-14
## sigma_stratadata[, facVar]11013 13.96911978 2.405816e-44
## sigma_stratadata[, facVar]11014 12.41797990 2.087665e-35
## sigma_stratadata[, facVar]11016 13.52939274 1.048865e-41
## sigma_stratadata[, facVar]11017 12.76291186 2.641393e-37
## sigma_stratadata[, facVar]11018 13.72889215 6.816788e-43
## sigma_stratadata[, facVar]11020 11.89533044 1.251567e-32
## sigma_stratadata[, facVar]11021 10.36149664 3.711092e-25
## sigma_stratadata[, facVar]11022 2.40570704 1.614120e-02
fit_normal.coordinate3.premeno$res_normal
## Estimate Std.Error
## (Intercept) -6.030681e-01 4.916567e-01
## prs_scaled 4.834290e-01 1.999589e-01
## PC1 -2.437040e-02 2.355753e-02
## PC2 -3.267051e-02 2.496128e-02
## PC3 3.962000e-02 3.133163e-02
## PC4 3.406917e-03 1.493361e-02
## PC5 -7.474407e-03 9.384280e-03
## PC6 7.488371e-02 3.332560e-02
## PC7 2.409037e-02 1.493817e-02
## PC8 -6.084248e-02 2.176378e-02
## PC9 -2.354267e-04 1.494811e-02
## PC10 -1.769046e-02 2.750409e-02
## agegroups[45,50) 3.792724e-01 1.285723e-01
## agegroups[50,80) 2.718982e-01 1.572277e-01
## n.children.scale 1.748595e-01 9.971471e-02
## birth.x 5.197520e-02 7.939960e-02
## birth.y 6.900374e-02 9.191738e-02
## age.firstbirth.group[25,35) 2.315620e-01 1.670917e-01
## age.firstbirth.group[35,80) 5.212595e-01 2.448755e-01
## age.firstbirth.group[80,1e+03) 7.394951e-01 2.770383e-01
## height.scale 7.982300e-02 5.820120e-02
## age.menarche.scale -2.941666e-02 5.740054e-02
## factor(oc.cate3)1 -5.201128e-01 2.448579e-01
## factor(oc.cate3)2 -5.066867e-01 2.345209e-01
## factor(oc.cate3)3 -1.586910e-01 2.327571e-01
## factor(oc.cate3)4 -7.995669e-02 2.151473e-01
## BMI.scale 4.004497e-02 5.848709e-02
## assessment_center10003 1.434424e+01 1.342782e+03
## assessment_center11002 2.702606e-01 4.450792e-01
## assessment_center11003 6.494632e-01 4.444431e-01
## assessment_center11004 1.837279e-01 4.344730e-01
## assessment_center11005 2.445649e-01 4.280193e-01
## assessment_center11006 3.886089e-01 4.081083e-01
## assessment_center11007 5.943782e-02 3.777004e-01
## assessment_center11008 4.421748e-01 3.888315e-01
## assessment_center11009 2.829191e-01 3.853465e-01
## assessment_center11010 2.620463e-01 3.611014e-01
## assessment_center11011 -1.232852e-01 3.697448e-01
## assessment_center11012 -1.497323e-01 5.410006e-01
## assessment_center11013 3.136287e-01 3.949667e-01
## assessment_center11014 -5.844650e-02 4.045028e-01
## assessment_center11016 -1.599245e-01 3.961270e-01
## assessment_center11017 -6.157565e-01 4.166125e-01
## assessment_center11018 -3.165940e-01 3.953370e-01
## assessment_center11020 -4.469887e-01 4.290099e-01
## assessment_center11021 -1.816574e-01 4.440861e-01
## assessment_center11022 -1.425224e+01 9.138673e+02
## alcohol 8.217321e-02 1.639616e-01
## prs_scaled:birth.x -2.407554e-02 6.340013e-02
## prs_scaled:birth.y 2.758555e-03 6.345298e-02
## prs_scaled:factor(oc.cate3)1 1.240336e-01 1.665844e-01
## prs_scaled:factor(oc.cate3)2 4.736964e-02 1.601489e-01
## prs_scaled:factor(oc.cate3)3 -8.375771e-02 1.557043e-01
## prs_scaled:factor(oc.cate3)4 -9.236681e-02 1.422857e-01
## prs_scaled:age.menarche.scale -2.551287e-02 3.999325e-02
## prs_scaled:BMI.scale -3.058051e-02 4.016082e-02
## prs_scaled:agegroups[45,50) 8.086746e-03 9.065731e-02
## prs_scaled:agegroups[50,80) 1.234713e-01 1.105198e-01
## prs_scaled:alcohol 6.570420e-02 1.178867e-01
## prs_scaled:height.scale -3.861275e-03 4.061332e-02
## prs_scaled:n.children.scale 1.638361e-02 6.954255e-02
## prs_scaled:age.firstbirth.group[25,35) -1.183316e-02 1.193089e-01
## prs_scaled:age.firstbirth.group[35,80) 4.516450e-02 1.674385e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 5.011693e-03 1.946767e-01
## eta_(Intercept) -3.012850e-01 8.307733e-02
## eta_PC1 -5.835038e-03 6.700790e-03
## eta_PC2 -3.508714e-04 9.127782e-03
## eta_PC3 1.206375e-02 1.400716e-02
## eta_PC4 4.349079e-03 6.453067e-03
## eta_PC5 -2.451736e-03 4.098460e-03
## eta_PC6 -5.950954e-04 1.514636e-02
## eta_PC7 8.120735e-03 6.599742e-03
## eta_PC8 -1.550074e-03 9.835756e-03
## eta_PC9 -3.789679e-04 6.533442e-03
## eta_PC10 -1.907775e-03 1.248031e-02
## eta_birth.x 1.032018e-02 4.173253e-02
## eta_birth.y 5.973132e-03 4.466633e-02
## sigma_stratadata[, facVar]11001 9.156277e-01 8.857062e-02
## sigma_stratadata[, facVar]10003 2.638237e-01 2.233296e-01
## sigma_stratadata[, facVar]11002 9.443325e-01 8.814163e-02
## sigma_stratadata[, facVar]11003 9.685271e-01 8.174889e-02
## sigma_stratadata[, facVar]11004 9.699736e-01 7.459925e-02
## sigma_stratadata[, facVar]11005 9.428483e-01 7.627387e-02
## sigma_stratadata[, facVar]11006 9.705090e-01 7.559002e-02
## sigma_stratadata[, facVar]11007 9.222382e-01 5.803860e-02
## sigma_stratadata[, facVar]11008 9.370973e-01 6.470263e-02
## sigma_stratadata[, facVar]11009 9.960743e-01 6.159429e-02
## sigma_stratadata[, facVar]11010 1.020156e+00 5.516453e-02
## sigma_stratadata[, facVar]11011 9.426153e-01 5.209988e-02
## sigma_stratadata[, facVar]11012 8.892506e-01 1.192046e-01
## sigma_stratadata[, facVar]11013 9.018776e-01 6.462057e-02
## sigma_stratadata[, facVar]11014 9.128749e-01 7.355572e-02
## sigma_stratadata[, facVar]11016 9.358242e-01 6.912200e-02
## sigma_stratadata[, facVar]11017 1.067621e+00 8.368633e-02
## sigma_stratadata[, facVar]11018 9.229090e-01 6.717033e-02
## sigma_stratadata[, facVar]11020 1.101659e+00 9.250257e-02
## sigma_stratadata[, facVar]11021 9.284805e-01 8.979264e-02
## sigma_stratadata[, facVar]11022 7.081647e-01 2.943990e-01
## Z.value Pvalue
## (Intercept) -1.22660405 2.199714e-01
## prs_scaled 2.41764162 1.562145e-02
## PC1 -1.03450564 3.008998e-01
## PC2 -1.30884737 1.905861e-01
## PC3 1.26453700 2.060373e-01
## PC4 0.22813752 8.195393e-01
## PC5 -0.79648168 4.257521e-01
## PC6 2.24703271 2.463794e-02
## PC7 1.61267161 1.068159e-01
## PC8 -2.79558417 5.180601e-03
## PC9 -0.01574960 9.874342e-01
## PC10 -0.64319377 5.200984e-01
## agegroups[45,50) 2.94987534 3.179022e-03
## agegroups[50,80) 1.72932719 8.375055e-02
## n.children.scale 1.75359754 7.949949e-02
## birth.x 0.65460281 5.127235e-01
## birth.y 0.75071478 4.528243e-01
## age.firstbirth.group[25,35) 1.38583773 1.657965e-01
## age.firstbirth.group[35,80) 2.12867160 3.328144e-02
## age.firstbirth.group[80,1e+03) 2.66928788 7.601227e-03
## height.scale 1.37150098 1.702188e-01
## age.menarche.scale -0.51248061 6.083147e-01
## factor(oc.cate3)1 -2.12414157 3.365831e-02
## factor(oc.cate3)2 -2.16051863 3.073254e-02
## factor(oc.cate3)3 -0.68178825 4.953729e-01
## factor(oc.cate3)4 -0.37163691 7.101632e-01
## BMI.scale 0.68468042 4.935456e-01
## assessment_center10003 0.01068248 9.914768e-01
## assessment_center11002 0.60721902 5.437056e-01
## assessment_center11003 1.46129665 1.439340e-01
## assessment_center11004 0.42287538 6.723862e-01
## assessment_center11005 0.57138763 5.677369e-01
## assessment_center11006 0.95222001 3.409854e-01
## assessment_center11007 0.15736765 8.749551e-01
## assessment_center11008 1.13718873 2.554594e-01
## assessment_center11009 0.73419393 4.628306e-01
## assessment_center11010 0.72568633 4.680311e-01
## assessment_center11011 -0.33343310 7.388074e-01
## assessment_center11012 -0.27676916 7.819574e-01
## assessment_center11013 0.79406377 4.271583e-01
## assessment_center11014 -0.14448974 8.851138e-01
## assessment_center11016 -0.40372032 6.864184e-01
## assessment_center11017 -1.47800763 1.394057e-01
## assessment_center11018 -0.80082045 4.232356e-01
## assessment_center11020 -1.04190783 2.974544e-01
## assessment_center11021 -0.40905902 6.824964e-01
## assessment_center11022 -0.01559553 9.875571e-01
## alcohol 0.50117342 6.162491e-01
## prs_scaled:birth.x -0.37973959 7.041387e-01
## prs_scaled:birth.y 0.04347401 9.653237e-01
## prs_scaled:factor(oc.cate3)1 0.74456901 4.565323e-01
## prs_scaled:factor(oc.cate3)2 0.29578496 7.673943e-01
## prs_scaled:factor(oc.cate3)3 -0.53792815 5.906267e-01
## prs_scaled:factor(oc.cate3)4 -0.64916433 5.162322e-01
## prs_scaled:age.menarche.scale -0.63792957 5.235195e-01
## prs_scaled:BMI.scale -0.76145134 4.463875e-01
## prs_scaled:agegroups[45,50) 0.08920125 9.289220e-01
## prs_scaled:agegroups[50,80) 1.11718696 2.639144e-01
## prs_scaled:alcohol 0.55735060 5.772879e-01
## prs_scaled:height.scale -0.09507411 9.242560e-01
## prs_scaled:n.children.scale 0.23559122 8.137499e-01
## prs_scaled:age.firstbirth.group[25,35) -0.09918087 9.209947e-01
## prs_scaled:age.firstbirth.group[35,80) 0.26973776 7.873620e-01
## prs_scaled:age.firstbirth.group[80,1e+03) 0.02574367 9.794618e-01
## eta_(Intercept) -3.62656115 2.872208e-04
## eta_PC1 -0.87079856 3.838641e-01
## eta_PC2 -0.03843994 9.693369e-01
## eta_PC3 0.86125636 3.890969e-01
## eta_PC4 0.67395541 5.003397e-01
## eta_PC5 -0.59820899 5.497005e-01
## eta_PC6 -0.03928966 9.686594e-01
## eta_PC7 1.23046249 2.185240e-01
## eta_PC8 -0.15759585 8.747753e-01
## eta_PC9 -0.05800432 9.537452e-01
## eta_PC10 -0.15286281 8.785065e-01
## eta_birth.x 0.24729333 8.046812e-01
## eta_birth.y 0.13372784 8.936178e-01
## sigma_stratadata[, facVar]11001 10.33782690 4.751907e-25
## sigma_stratadata[, facVar]10003 1.18132016 2.374756e-01
## sigma_stratadata[, facVar]11002 10.71380842 8.767901e-27
## sigma_stratadata[, facVar]11003 11.84758678 2.214772e-32
## sigma_stratadata[, facVar]11004 13.00245838 1.184726e-38
## sigma_stratadata[, facVar]11005 12.36135410 4.229711e-35
## sigma_stratadata[, facVar]11006 12.83911593 9.899852e-38
## sigma_stratadata[, facVar]11007 15.89008495 7.422692e-57
## sigma_stratadata[, facVar]11008 14.48314007 1.548579e-47
## sigma_stratadata[, facVar]11009 16.17153728 8.007507e-59
## sigma_stratadata[, facVar]11010 18.49297316 2.352206e-76
## sigma_stratadata[, facVar]11011 18.09246492 3.653733e-73
## sigma_stratadata[, facVar]11012 7.45986872 8.660873e-14
## sigma_stratadata[, facVar]11013 13.95651003 2.871547e-44
## sigma_stratadata[, facVar]11014 12.41065947 2.287608e-35
## sigma_stratadata[, facVar]11016 13.53873205 9.236953e-42
## sigma_stratadata[, facVar]11017 12.75741506 2.834519e-37
## sigma_stratadata[, facVar]11018 13.73983149 5.861205e-43
## sigma_stratadata[, facVar]11020 11.90949882 1.056101e-32
## sigma_stratadata[, facVar]11021 10.34027380 4.632122e-25
## sigma_stratadata[, facVar]11022 2.40545922 1.615215e-02
#Logistic regression on the case-control samples
fit_normal.coordinate1.premeno$res_glm
## Estimate Std. Error
## (Intercept) -8.243300e-01 4.742918e-01
## prs_scaled 6.022829e-01 2.428489e-01
## PC1 -2.882915e-02 2.459981e-02
## PC2 -3.786671e-02 2.544744e-02
## PC3 4.096103e-02 3.184662e-02
## PC4 3.578548e-03 1.534377e-02
## PC5 -7.816834e-03 9.467848e-03
## PC6 6.479887e-02 3.358688e-02
## PC7 2.282345e-02 1.474043e-02
## PC8 -5.607639e-02 2.197096e-02
## PC9 -5.395428e-04 1.499070e-02
## PC10 -2.205444e-02 2.793398e-02
## agegroups[45,50) 3.333805e-01 1.313576e-01
## agegroups[50,80) 2.778238e-01 1.617468e-01
## n.children.scale 1.302927e-01 1.009571e-01
## birth.x 5.469061e-02 8.085656e-02
## birth.y 7.141507e-02 9.409417e-02
## age.firstbirth.group[25,35) 2.398731e-01 1.691833e-01
## age.firstbirth.group[35,80) 5.616887e-01 2.508323e-01
## age.firstbirth.group[80,1e+03) 6.871900e-01 2.808257e-01
## height.scale 7.843799e-02 5.929138e-02
## age.menarche.scale -1.531947e-02 5.836095e-02
## length.oc.scale 9.464637e-02 5.862197e-02
## BMI.scale 4.221617e-02 5.946850e-02
## assessment_center10003 1.441583e+01 8.827435e+02
## assessment_center11002 3.010470e-01 4.611352e-01
## assessment_center11003 6.126563e-01 4.573325e-01
## assessment_center11004 2.219473e-01 4.505146e-01
## assessment_center11005 2.168008e-01 4.424195e-01
## assessment_center11006 2.638907e-01 4.212699e-01
## assessment_center11007 1.448371e-01 3.924672e-01
## assessment_center11008 6.200225e-01 4.042327e-01
## assessment_center11009 2.306281e-01 3.992872e-01
## assessment_center11010 2.858121e-01 3.745669e-01
## assessment_center11011 -6.465953e-02 3.843211e-01
## assessment_center11012 -2.025977e-01 5.578473e-01
## assessment_center11013 1.488063e-01 4.093823e-01
## assessment_center11014 -3.556650e-02 4.182090e-01
## assessment_center11016 -7.483747e-02 4.088478e-01
## assessment_center11017 -6.547522e-01 4.332296e-01
## assessment_center11018 -3.959249e-01 4.094623e-01
## assessment_center11020 -4.903342e-01 4.444563e-01
## assessment_center11021 -2.653443e-01 4.574402e-01
## assessment_center11022 -1.422271e+01 4.900044e+02
## alcohol 6.694736e-02 1.674530e-01
## prs_scaled:birth.x -2.748162e-02 7.095202e-02
## prs_scaled:birth.y -5.962796e-03 6.966354e-02
## prs_scaled:length.oc.scale -1.382725e-02 6.203834e-02
## prs_scaled:age.menarche.scale 1.631170e-02 6.441085e-02
## prs_scaled:BMI.scale -1.194260e-02 6.412914e-02
## prs_scaled:agegroups[45,50) -9.626903e-02 1.406591e-01
## prs_scaled:agegroups[50,80) 2.121685e-01 1.739780e-01
## prs_scaled:alcohol -5.782103e-02 1.874503e-01
## prs_scaled:height.scale 5.034938e-02 6.272358e-02
## prs_scaled:n.children.scale -1.020612e-01 1.103808e-01
## prs_scaled:age.firstbirth.group[25,35) 1.029491e-01 1.771755e-01
## prs_scaled:age.firstbirth.group[35,80) 1.181946e-01 2.550182e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -2.153718e-01 2.949661e-01
## z value Pr(>|z|)
## (Intercept) -1.73802299 0.08220676
## prs_scaled 2.48007277 0.01313556
## PC1 -1.17192599 0.24122677
## PC2 -1.48803590 0.13674143
## PC3 1.28619679 0.19837439
## PC4 0.23322476 0.81558688
## PC5 -0.82561888 0.40902032
## PC6 1.92929138 0.05369470
## PC7 1.54835736 0.12153628
## PC8 -2.55229574 0.01070156
## PC9 -0.03599184 0.97128886
## PC10 -0.78952005 0.42980812
## agegroups[45,50) 2.53796151 0.01115002
## agegroups[50,80) 1.71764679 0.08586106
## n.children.scale 1.29057503 0.19685108
## birth.x 0.67639052 0.49879274
## birth.y 0.75897442 0.44786786
## age.firstbirth.group[25,35) 1.41782975 0.15624048
## age.firstbirth.group[35,80) 2.23930013 0.02513639
## age.firstbirth.group[80,1e+03) 2.44703417 0.01440372
## height.scale 1.32292403 0.18586064
## age.menarche.scale -0.26249519 0.79293969
## length.oc.scale 1.61452050 0.10641457
## BMI.scale 0.70989123 0.47777159
## assessment_center10003 0.01633072 0.98697055
## assessment_center11002 0.65283883 0.51386019
## assessment_center11003 1.33962981 0.18036573
## assessment_center11004 0.49265284 0.62225791
## assessment_center11005 0.49003439 0.62410956
## assessment_center11006 0.62641714 0.53104137
## assessment_center11007 0.36904258 0.71209599
## assessment_center11008 1.53382562 0.12507256
## assessment_center11009 0.57759949 0.56353455
## assessment_center11010 0.76304696 0.44543539
## assessment_center11011 -0.16824349 0.86639173
## assessment_center11012 -0.36317764 0.71647219
## assessment_center11013 0.36348989 0.71623896
## assessment_center11014 -0.08504480 0.93222577
## assessment_center11016 -0.18304479 0.85476287
## assessment_center11017 -1.51132859 0.13070475
## assessment_center11018 -0.96693872 0.33357467
## assessment_center11020 -1.10322248 0.26993056
## assessment_center11021 -0.58006337 0.56187188
## assessment_center11022 -0.02902568 0.97684411
## alcohol 0.39979789 0.68930538
## prs_scaled:birth.x -0.38732679 0.69851429
## prs_scaled:birth.y -0.08559421 0.93178900
## prs_scaled:length.oc.scale -0.22288231 0.82362711
## prs_scaled:age.menarche.scale 0.25324466 0.80007916
## prs_scaled:BMI.scale -0.18622728 0.85226653
## prs_scaled:agegroups[45,50) -0.68441378 0.49371392
## prs_scaled:agegroups[50,80) 1.21951343 0.22264938
## prs_scaled:alcohol -0.30846053 0.75773193
## prs_scaled:height.scale 0.80271849 0.42213746
## prs_scaled:n.children.scale -0.92462795 0.35515947
## prs_scaled:age.firstbirth.group[25,35) 0.58105736 0.56120179
## prs_scaled:age.firstbirth.group[35,80) 0.46347521 0.64302378
## prs_scaled:age.firstbirth.group[80,1e+03) -0.73015763 0.46529384
fit_normal.coordinate2.premeno$res_glm
## Estimate Std. Error
## (Intercept) -5.899455e-01 5.135351e-01
## prs_scaled 5.058746e-01 3.063313e-01
## PC1 -2.681831e-02 2.477276e-02
## PC2 -3.554226e-02 2.584053e-02
## PC3 4.149386e-02 3.201562e-02
## PC4 3.524074e-03 1.536907e-02
## PC5 -8.745633e-03 9.499192e-03
## PC6 7.084685e-02 3.372489e-02
## PC7 2.338551e-02 1.478529e-02
## PC8 -5.697421e-02 2.207109e-02
## PC9 -6.525635e-04 1.506272e-02
## PC10 -2.074899e-02 2.799405e-02
## agegroups[45,50) 3.515697e-01 1.317263e-01
## agegroups[50,80) 3.036412e-01 1.625602e-01
## n.children.scale 1.340794e-01 1.014205e-01
## birth.x 6.298543e-02 8.128115e-02
## birth.y 7.452464e-02 9.448404e-02
## age.firstbirth.group[25,35) 2.500018e-01 1.700084e-01
## age.firstbirth.group[35,80) 5.341185e-01 2.517843e-01
## age.firstbirth.group[80,1e+03) 6.579923e-01 2.827994e-01
## height.scale 8.169514e-02 5.960098e-02
## age.menarche.scale -1.607536e-02 5.864723e-02
## factor(oc.cate2)1 -5.110098e-01 2.220163e-01
## factor(oc.cate2)2 -8.894853e-02 2.134113e-01
## BMI.scale 4.572423e-02 5.988413e-02
## assessment_center10003 1.431802e+01 8.827435e+02
## assessment_center11002 2.945649e-01 4.631877e-01
## assessment_center11003 5.907679e-01 4.601427e-01
## assessment_center11004 2.010841e-01 4.521563e-01
## assessment_center11005 2.283557e-01 4.435372e-01
## assessment_center11006 2.851812e-01 4.233220e-01
## assessment_center11007 1.286208e-01 3.940284e-01
## assessment_center11008 6.189153e-01 4.063733e-01
## assessment_center11009 2.205079e-01 4.016102e-01
## assessment_center11010 2.537691e-01 3.762147e-01
## assessment_center11011 -8.569009e-02 3.862009e-01
## assessment_center11012 -1.267790e-01 5.637605e-01
## assessment_center11013 1.594563e-01 4.106897e-01
## assessment_center11014 -5.641216e-02 4.197684e-01
## assessment_center11016 -9.716454e-02 4.108805e-01
## assessment_center11017 -6.813809e-01 4.350066e-01
## assessment_center11018 -4.192676e-01 4.113160e-01
## assessment_center11020 -4.767572e-01 4.462915e-01
## assessment_center11021 -2.834204e-01 4.588754e-01
## assessment_center11022 -1.423604e+01 4.791850e+02
## alcohol 7.843716e-02 1.686531e-01
## prs_scaled:birth.x -3.493772e-02 7.124272e-02
## prs_scaled:birth.y -6.316855e-03 7.000364e-02
## prs_scaled:factor(oc.cate2)1 1.262087e-01 2.204809e-01
## prs_scaled:factor(oc.cate2)2 8.795263e-02 2.112897e-01
## prs_scaled:age.menarche.scale 8.210232e-03 6.473349e-02
## prs_scaled:BMI.scale -2.369488e-02 6.407806e-02
## prs_scaled:agegroups[45,50) -1.006656e-01 1.410064e-01
## prs_scaled:agegroups[50,80) 2.062175e-01 1.740766e-01
## prs_scaled:alcohol -5.657852e-02 1.879799e-01
## prs_scaled:height.scale 4.425442e-02 6.304676e-02
## prs_scaled:n.children.scale -8.949471e-02 1.114801e-01
## prs_scaled:age.firstbirth.group[25,35) 1.041917e-01 1.776863e-01
## prs_scaled:age.firstbirth.group[35,80) 1.138125e-01 2.556207e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -1.739911e-01 2.978507e-01
## z value Pr(>|z|)
## (Intercept) -1.14879282 0.250641421
## prs_scaled 1.65139708 0.098657521
## PC1 -1.08257266 0.278998147
## PC2 -1.37544667 0.168993008
## PC3 1.29605015 0.194958207
## PC4 0.22929643 0.818638526
## PC5 -0.92067122 0.357222108
## PC6 2.10072872 0.035664787
## PC7 1.58167348 0.113724129
## PC8 -2.58139513 0.009840188
## PC9 -0.04332308 0.965443997
## PC10 -0.74119296 0.458576452
## agegroups[45,50) 2.66894114 0.007609078
## agegroups[50,80) 1.86786918 0.061780308
## n.children.scale 1.32201462 0.186163282
## birth.x 0.77490814 0.438393941
## birth.y 0.78875373 0.430255960
## age.firstbirth.group[25,35) 1.47052624 0.141419285
## age.firstbirth.group[35,80) 2.12133303 0.033893786
## age.firstbirth.group[80,1e+03) 2.32671058 0.019980674
## height.scale 1.37070143 0.170468048
## age.menarche.scale -0.27410266 0.784005733
## factor(oc.cate2)1 -2.30167634 0.021353431
## factor(oc.cate2)2 -0.41679390 0.676829162
## BMI.scale 0.76354507 0.445138393
## assessment_center10003 0.01621991 0.987058948
## assessment_center11002 0.63595141 0.524808092
## assessment_center11003 1.28387967 0.199184062
## assessment_center11004 0.44472256 0.656520262
## assessment_center11005 0.51485117 0.606657026
## assessment_center11006 0.67367445 0.500518310
## assessment_center11007 0.32642510 0.744102751
## assessment_center11008 1.52302158 0.127753306
## assessment_center11009 0.54905935 0.582964719
## assessment_center11010 0.67453260 0.499972764
## assessment_center11011 -0.22187955 0.824407650
## assessment_center11012 -0.22488095 0.822071892
## assessment_center11013 0.38826456 0.697820263
## assessment_center11014 -0.13438877 0.893095161
## assessment_center11016 -0.23647885 0.813061114
## assessment_center11017 -1.56636927 0.117262193
## assessment_center11018 -1.01933208 0.308045341
## assessment_center11020 -1.06826401 0.285401438
## assessment_center11021 -0.61764131 0.536811808
## assessment_center11022 -0.02970886 0.976299249
## alcohol 0.46507996 0.641874195
## prs_scaled:birth.x -0.49040407 0.623847999
## prs_scaled:birth.y -0.09023608 0.928099612
## prs_scaled:factor(oc.cate2)1 0.57242440 0.567034491
## prs_scaled:factor(oc.cate2)2 0.41626565 0.677215622
## prs_scaled:age.menarche.scale 0.12683128 0.899073935
## prs_scaled:BMI.scale -0.36978147 0.711545325
## prs_scaled:agegroups[45,50) -0.71390804 0.475284044
## prs_scaled:agegroups[50,80) 1.18463634 0.236161261
## prs_scaled:alcohol -0.30098174 0.763428422
## prs_scaled:height.scale 0.70193021 0.482722687
## prs_scaled:n.children.scale -0.80278662 0.422098079
## prs_scaled:age.firstbirth.group[25,35) 0.58638032 0.557619965
## prs_scaled:age.firstbirth.group[35,80) 0.44523979 0.656146472
## prs_scaled:age.firstbirth.group[80,1e+03) -0.58415532 0.559115821
fit_normal.coordinate3.premeno$res_glm
## Estimate Std. Error
## (Intercept) -5.852458e-01 5.136339e-01
## prs_scaled 4.981781e-01 3.070549e-01
## PC1 -2.685566e-02 2.474547e-02
## PC2 -3.551844e-02 2.585408e-02
## PC3 4.210044e-02 3.206285e-02
## PC4 3.675404e-03 1.538254e-02
## PC5 -8.763056e-03 9.521437e-03
## PC6 7.020305e-02 3.376372e-02
## PC7 2.292026e-02 1.481660e-02
## PC8 -5.685700e-02 2.207473e-02
## PC9 -6.441159e-04 1.508002e-02
## PC10 -2.027194e-02 2.809406e-02
## agegroups[45,50) 3.500074e-01 1.319578e-01
## agegroups[50,80) 3.043384e-01 1.627712e-01
## n.children.scale 1.344238e-01 1.015162e-01
## birth.x 6.344343e-02 8.133537e-02
## birth.y 7.431559e-02 9.465812e-02
## age.firstbirth.group[25,35) 2.497953e-01 1.704622e-01
## age.firstbirth.group[35,80) 5.310076e-01 2.518733e-01
## age.firstbirth.group[80,1e+03) 6.520145e-01 2.832351e-01
## height.scale 8.184770e-02 5.963968e-02
## age.menarche.scale -1.649879e-02 5.873583e-02
## factor(oc.cate3)1 -5.295831e-01 2.502849e-01
## factor(oc.cate3)2 -5.021454e-01 2.392394e-01
## factor(oc.cate3)3 -1.144676e-01 2.389966e-01
## factor(oc.cate3)4 -7.603932e-02 2.203070e-01
## BMI.scale 4.632786e-02 6.023004e-02
## assessment_center10003 1.434424e+01 8.827435e+02
## assessment_center11002 2.935678e-01 4.637559e-01
## assessment_center11003 5.838198e-01 4.606139e-01
## assessment_center11004 1.987220e-01 4.527261e-01
## assessment_center11005 2.291045e-01 4.445396e-01
## assessment_center11006 2.844610e-01 4.241983e-01
## assessment_center11007 1.289784e-01 3.946885e-01
## assessment_center11008 6.179574e-01 4.071907e-01
## assessment_center11009 2.158629e-01 4.031041e-01
## assessment_center11010 2.529012e-01 3.770603e-01
## assessment_center11011 -8.419909e-02 3.869854e-01
## assessment_center11012 -1.277287e-01 5.642854e-01
## assessment_center11013 1.567140e-01 4.110588e-01
## assessment_center11014 -5.349773e-02 4.203180e-01
## assessment_center11016 -9.256728e-02 4.114040e-01
## assessment_center11017 -6.922614e-01 4.358152e-01
## assessment_center11018 -4.180248e-01 4.120689e-01
## assessment_center11020 -4.806726e-01 4.469895e-01
## assessment_center11021 -2.853067e-01 4.593924e-01
## assessment_center11022 -1.425223e+01 4.802748e+02
## alcohol 7.848826e-02 1.689775e-01
## prs_scaled:birth.x -3.492013e-02 7.125984e-02
## prs_scaled:birth.y -5.714095e-03 7.014386e-02
## prs_scaled:factor(oc.cate3)1 1.612311e-01 2.567951e-01
## prs_scaled:factor(oc.cate3)2 1.062818e-01 2.375471e-01
## prs_scaled:factor(oc.cate3)3 1.301479e-01 2.401129e-01
## prs_scaled:factor(oc.cate3)4 6.434936e-02 2.198784e-01
## prs_scaled:age.menarche.scale 9.283290e-03 6.495195e-02
## prs_scaled:BMI.scale -2.276658e-02 6.442835e-02
## prs_scaled:agegroups[45,50) -1.006707e-01 1.413755e-01
## prs_scaled:agegroups[50,80) 2.026325e-01 1.746399e-01
## prs_scaled:alcohol -5.149641e-02 1.889183e-01
## prs_scaled:height.scale 4.507351e-02 6.317919e-02
## prs_scaled:n.children.scale -9.011938e-02 1.120537e-01
## prs_scaled:age.firstbirth.group[25,35) 1.068376e-01 1.780441e-01
## prs_scaled:age.firstbirth.group[35,80) 1.188177e-01 2.565879e-01
## prs_scaled:age.firstbirth.group[80,1e+03) -1.667526e-01 3.002657e-01
## z value Pr(>|z|)
## (Intercept) -1.13942200 0.254527182
## prs_scaled 1.62243960 0.104709255
## PC1 -1.08527573 0.277799554
## PC2 -1.37380418 0.169502484
## PC3 1.31305993 0.189162753
## PC4 0.23893343 0.811157201
## PC5 -0.92035021 0.357389778
## PC6 2.07924499 0.037594838
## PC7 1.54693058 0.121879985
## PC8 -2.57566017 0.010004892
## PC9 -0.04271319 0.965930164
## PC10 -0.72157377 0.470556569
## agegroups[45,50) 2.65241868 0.007991738
## agegroups[50,80) 1.86973128 0.061521144
## n.children.scale 1.32416176 0.185449329
## birth.x 0.78002264 0.435377547
## birth.y 0.78509470 0.432398048
## age.firstbirth.group[25,35) 1.46540013 0.142811783
## age.firstbirth.group[35,80) 2.10823289 0.035010849
## age.firstbirth.group[80,1e+03) 2.30202580 0.021333718
## height.scale 1.37236993 0.169948307
## age.menarche.scale -0.28089820 0.778788480
## factor(oc.cate3)1 -2.11592107 0.034351521
## factor(oc.cate3)2 -2.09892459 0.035823549
## factor(oc.cate3)3 -0.47895054 0.631973815
## factor(oc.cate3)4 -0.34515171 0.729980317
## BMI.scale 0.76918189 0.441785339
## assessment_center10003 0.01624961 0.987035260
## assessment_center11002 0.63302216 0.526719171
## assessment_center11003 1.26748180 0.204983067
## assessment_center11004 0.43894531 0.660701165
## assessment_center11005 0.51537466 0.606291236
## assessment_center11006 0.67058491 0.502484997
## assessment_center11007 0.32678516 0.743830384
## assessment_center11008 1.51761197 0.129112247
## assessment_center11009 0.53550177 0.592302935
## assessment_center11010 0.67071804 0.502400166
## assessment_center11011 -0.21757691 0.827758776
## assessment_center11012 -0.22635482 0.820925461
## assessment_center11013 0.38124471 0.703021674
## assessment_center11014 -0.12727917 0.898719450
## assessment_center11016 -0.22500335 0.821976672
## assessment_center11017 -1.58842859 0.112189456
## assessment_center11018 -1.01445345 0.310366429
## assessment_center11020 -1.07535547 0.282215608
## assessment_center11021 -0.62105220 0.534565279
## assessment_center11022 -0.02967516 0.976326121
## alcohol 0.46448934 0.642297192
## prs_scaled:birth.x -0.49003947 0.624105966
## prs_scaled:birth.y -0.08146251 0.935074140
## prs_scaled:factor(oc.cate3)1 0.62785911 0.530096240
## prs_scaled:factor(oc.cate3)2 0.44741343 0.654576578
## prs_scaled:factor(oc.cate3)3 0.54202801 0.587799210
## prs_scaled:factor(oc.cate3)4 0.29265890 0.769782891
## prs_scaled:age.menarche.scale 0.14292550 0.886349023
## prs_scaled:BMI.scale -0.35336285 0.723816432
## prs_scaled:agegroups[45,50) -0.71207975 0.476415394
## prs_scaled:agegroups[50,80) 1.16028767 0.245931704
## prs_scaled:alcohol -0.27258558 0.785171798
## prs_scaled:height.scale 0.71342338 0.475583809
## prs_scaled:n.children.scale -0.80425160 0.421251681
## prs_scaled:age.firstbirth.group[25,35) 0.60006240 0.548464649
## prs_scaled:age.firstbirth.group[35,80) 0.46306806 0.643315585
## prs_scaled:age.firstbirth.group[80,1e+03) -0.55535010 0.578655220
summary.caseonly=function (parms, sd, sided = 2)
{
if (sided != 1)
sided <- 2
cols <- c("Estimate", "Std.Error", "Z.value", "Pvalue")
n <- length(parms)
ret <- matrix(data = NA, nrow = n, ncol = 4)
pnames <- c("prs",paste0("prs:",names(parms)[-1]))
rownames(ret) <- pnames
colnames(ret) <- cols
ret[, 1] <- parms
if (is.null(pnames))
pnames <- 1:n
cov <- sd
ret[, 2] <- cov
ret[, 3] <- parms/cov
ret[, 4] <- sided * pnorm(abs(ret[, 3]), lower.tail = FALSE)
ret
}
dat_caseonly=dat_test_casecontrol.coordinate[which(dat_test_casecontrol.coordinate$breast_cancer==1),]
fit_caseonly <- lm(prs_scaled~PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10+agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+length.oc.scale+BMI.scale+assessment_center+alcohol,data=dat_caseonly)
beta_int=fit_caseonly$coefficients[-1]/(sd(fit_caseonly$residuals))^2
sd_int=summary(fit_caseonly)$coef[-1,2]/(sd(fit_caseonly$residuals))^2
mean_prs=mean(dat_test_complete$prs_scaled)
beta_prs=(fit_caseonly$coefficients[1]-mean_prs)/(sd(fit_caseonly$residuals))^2
sd_prs= sqrt(( (summary(fit_caseonly)$coef[1,2])^2 +(sd(fit_caseonly$residuals))^2/dim(dat_test_complete)[1]) / (sd(fit_caseonly$residuals))^4)
res_caseonly_pre=summary.caseonly(parms = c(beta_prs,beta_int),sd=c(sd_prs,sd_int))
print(res_caseonly_pre)
## Estimate Std.Error Z.value
## prs 0.288358114 0.370143026 0.77904511
## prs:PC1 0.020993351 0.019732921 1.06387445
## prs:PC2 0.009377135 0.017038174 0.55036031
## prs:PC3 0.021167924 0.021642056 0.97809207
## prs:PC4 0.020634087 0.011492329 1.79546610
## prs:PC5 -0.011494856 0.007050321 -1.63040186
## prs:PC6 0.020195763 0.026156378 0.77211619
## prs:PC7 0.001354234 0.011707255 0.11567481
## prs:PC8 -0.001234178 0.017125764 -0.07206559
## prs:PC9 0.011964244 0.010879514 1.09970386
## prs:PC10 0.022415221 0.020179276 1.11080407
## prs:agegroups[45,50) -0.014085161 0.099330705 -0.14180068
## prs:agegroups[50,80) 0.098439939 0.122081159 0.80634833
## prs:n.children.scale 0.026730115 0.077300598 0.34579441
## prs:birth.x -0.068762916 0.059257018 -1.16041809
## prs:birth.y 0.001594965 0.067425920 0.02365507
## prs:age.firstbirth.group[25,35) -0.042621703 0.131747036 -0.32351167
## prs:age.firstbirth.group[35,80) 0.057033374 0.183629818 0.31058885
## prs:age.firstbirth.group[80,1e+03) -0.003308597 0.217378444 -0.01522045
## prs:height.scale -0.012664575 0.043830390 -0.28894506
## prs:age.menarche.scale -0.037101842 0.044630475 -0.83131184
## prs:length.oc.scale -0.097716992 0.043760733 -2.23298342
## prs:BMI.scale -0.042504338 0.043124649 -0.98561586
## prs:assessment_center10003 0.016176505 1.164487188 0.01389153
## prs:assessment_center11002 0.247358460 0.336514382 0.73506059
## prs:assessment_center11003 0.382857900 0.325890497 1.17480535
## prs:assessment_center11004 -0.121073196 0.339052122 -0.35709317
## prs:assessment_center11005 0.242223822 0.329171672 0.73585865
## prs:assessment_center11006 0.318100720 0.310702156 1.02381240
## prs:assessment_center11007 0.145305686 0.295915861 0.49103717
## prs:assessment_center11008 -0.207194534 0.294792850 -0.70284790
## prs:assessment_center11009 0.543733538 0.294352247 1.84722061
## prs:assessment_center11010 0.096825783 0.278643737 0.34748954
## prs:assessment_center11011 0.268334421 0.292303301 0.91799997
## prs:assessment_center11012 -0.325215195 0.434446531 -0.74857358
## prs:assessment_center11013 0.303140588 0.303097829 1.00014107
## prs:assessment_center11014 -0.194568580 0.319711402 -0.60857567
## prs:assessment_center11016 -0.132037806 0.319464911 -0.41330926
## prs:assessment_center11017 0.377750810 0.339585768 1.11238705
## prs:assessment_center11018 0.607162760 0.319620715 1.89963520
## prs:assessment_center11020 0.562240469 0.345512998 1.62726286
## prs:assessment_center11021 0.285523854 0.353849294 0.80690808
## prs:alcohol 0.054216366 0.131337435 0.41280208
## Pvalue
## prs 0.43595314
## prs:PC1 0.28738558
## prs:PC2 0.58207227
## prs:PC3 0.32802879
## prs:PC4 0.07257947
## prs:PC5 0.10301659
## prs:PC6 0.44004561
## prs:PC7 0.90791027
## prs:PC8 0.94254971
## prs:PC9 0.27146117
## prs:PC10 0.26665269
## prs:agegroups[45,50) 0.88723745
## prs:agegroups[50,80) 0.42004203
## prs:n.children.scale 0.72949722
## prs:birth.x 0.24587863
## prs:birth.y 0.98112775
## prs:age.firstbirth.group[25,35) 0.74630777
## prs:age.firstbirth.group[35,80) 0.75611320
## prs:age.firstbirth.group[80,1e+03) 0.98785631
## prs:height.scale 0.77262342
## prs:age.menarche.scale 0.40579749
## prs:length.oc.scale 0.02555004
## prs:BMI.scale 0.32432165
## prs:assessment_center10003 0.98891652
## prs:assessment_center11002 0.46230259
## prs:assessment_center11003 0.24007260
## prs:assessment_center11004 0.72102206
## prs:assessment_center11005 0.46181672
## prs:assessment_center11006 0.30592389
## prs:assessment_center11007 0.62340016
## prs:assessment_center11008 0.48215055
## prs:assessment_center11009 0.06471517
## prs:assessment_center11010 0.72822358
## prs:assessment_center11011 0.35861888
## prs:assessment_center11012 0.45411426
## prs:assessment_center11013 0.31724224
## prs:assessment_center11014 0.54280574
## prs:assessment_center11016 0.67938005
## prs:assessment_center11017 0.26597177
## prs:assessment_center11018 0.05748101
## prs:assessment_center11020 0.10368128
## prs:assessment_center11021 0.41971944
## prs:alcohol 0.67975163
fit_caseonly <- lm(prs_scaled~agegroups+n.children.scale+birth.x+birth.y+age.firstbirth.group+height.scale+age.menarche.scale+length.oc.scale+BMI.scale+alcohol,data=dat_caseonly)
beta_int=fit_caseonly$coefficients[-1]/(sd(fit_caseonly$residuals))^2
sd_int=summary(fit_caseonly)$coef[-1,2]/(sd(fit_caseonly$residuals))^2
beta_prs=(fit_caseonly$coefficients[1]-mean_prs)/(sd(fit_caseonly$residuals))^2
sd_prs= sqrt(( (summary(fit_caseonly)$coef[1,2])^2 +(sd(fit_caseonly$residuals))^2/dim(dat_test_complete)[1]) / (sd(fit_caseonly$residuals))^4)
res_caseonly=summary.caseonly(parms = c(beta_prs,beta_int),sd=c(sd_prs,sd_int))
print(res_caseonly)
## Estimate Std.Error Z.value
## prs 0.199809343 0.15769506 1.26706155
## prs:agegroups[45,50) 0.004834961 0.09228672 0.05239065
## prs:agegroups[50,80) 0.110419777 0.11291983 0.97785992
## prs:n.children.scale 0.003469724 0.07152696 0.04850932
## prs:birth.x 0.003299014 0.04479902 0.07364030
## prs:birth.y 0.012117665 0.04413193 0.27457815
## prs:age.firstbirth.group[25,35) -0.022184984 0.12207186 -0.18173709
## prs:age.firstbirth.group[35,80) 0.040040408 0.16920934 0.23663238
## prs:age.firstbirth.group[80,1e+03) -0.032134943 0.20073836 -0.16008372
## prs:height.scale -0.003559479 0.04044851 -0.08800024
## prs:age.menarche.scale -0.029090545 0.04183389 -0.69538231
## prs:length.oc.scale -0.083151529 0.04066973 -2.04455573
## prs:BMI.scale -0.028189123 0.03987906 -0.70686522
## prs:alcohol 0.081075510 0.12046285 0.67303328
## Pvalue
## prs 0.20513328
## prs:agegroups[45,50) 0.95821743
## prs:agegroups[50,80) 0.32814361
## prs:n.children.scale 0.96131034
## prs:birth.x 0.94129660
## prs:birth.y 0.78364036
## prs:age.firstbirth.group[25,35) 0.85578906
## prs:age.firstbirth.group[35,80) 0.81294200
## prs:age.firstbirth.group[80,1e+03) 0.87281513
## prs:height.scale 0.92987648
## prs:age.menarche.scale 0.48681575
## prs:length.oc.scale 0.04089868
## prs:BMI.scale 0.47965024
## prs:alcohol 0.50092612
Let’s summarize the results:
data1=array(0,c(4,4))
data1[1,]=fit_normal.coordinate1$res_normal[53,]
data1[2,]=summary(fit.int.all)$coef[53,]
data1[3,]=fit_normal.coordinate1$res_glm[53,]
data1[4,]=res_caseonly_post[25,]
rownames(data1)=c("retro_normal","logistic_regression_cohort","logistic_regression_casecontrol","case-only")
colnames(data1)=colnames(fit_normal.coordinate1$res_normal)
data2=array(0,c(4,4))
data2[1,]=fit_normal.coordinate1$res_normal[51,]
data2[2,]=summary(fit.int.all)$coef[51,]
data2[3,]=fit_normal.coordinate1$res_glm[51,]
data2[4,]=res_caseonly_post[17,]
rownames(data2)=c("retro_normal","logistic_regression_cohort","logistic_regression_casecontrol","case-only")
colnames(data2)=colnames(fit_normal.coordinate1$res_normal)
data3=array(0,c(4,4))
data3[1,]=fit_normal.coordinate1.premeno$res_normal[48,]
data3[2,]=summary(fit.int.all.premeno)$coef[49,]
data3[3,]=fit_normal.coordinate1.premeno$res_glm[48,]
data3[4,]=res_caseonly_pre[22,]
rownames(data3)=c("retro_normal","logistic_regression_cohort","logistic_regression_casecontrol","case-only")
colnames(data3)=colnames(fit_normal.coordinate1.premeno$res_normal)
We found interesting interactions between PRS and use of oral contraceptive use (Table 1) for both pre-menopause and post-menupause women, PRS and birth location in association with breast cancer (Table 2) for post-menopause women. In addition, in the cohort logistic regression, we found significant interaction between PRS and age at first birth.
library(knitr)
kable(data1,caption="PRS X Years of Oral Contraceptive Pill Use - Post-Menopause Women",digits=4)
Estimate | Std.Error | Z.value | Pvalue | |
---|---|---|---|---|
retro_normal | -0.0501 | 0.0240 | -2.0878 | 0.0368 |
logistic_regression_cohort | -0.0547 | 0.0234 | -2.3416 | 0.0192 |
logistic_regression_casecontrol | -0.0322 | 0.0362 | -0.8900 | 0.3735 |
case-only | -0.0502 | 0.0243 | -2.0603 | 0.0394 |
kable(data2,caption="PRS X Birth Location (east coordinate) - Post-Menopause Women",digits=4)
Estimate | Std.Error | Z.value | Pvalue | |
---|---|---|---|---|
retro_normal | -0.0785 | 0.0372 | -2.1107 | 0.0348 |
logistic_regression_cohort | -0.0682 | 0.0248 | -2.7508 | 0.0059 |
logistic_regression_casecontrol | -0.0901 | 0.0399 | -2.2559 | 0.0241 |
case-only | -0.0912 | 0.0329 | -2.7702 | 0.0056 |
kable(data3,caption="PRS X Years of Oral Contraceptive Pill Use - Pre-Menopause Women",digits=4)
Estimate | Std.Error | Z.value | Pvalue | |
---|---|---|---|---|
retro_normal | -0.0836 | 0.0394 | -2.1240 | 0.0337 |
logistic_regression_cohort | -0.0807 | 0.0374 | -2.1546 | 0.0312 |
logistic_regression_casecontrol | -0.0138 | 0.0620 | -0.2229 | 0.8236 |
case-only | -0.0977 | 0.0438 | -2.2330 | 0.0256 |
We additionally did sensitivity analysis for the years of OC use by categorizing them. We make two different categorical variables for the years of OC use by different intervals. The first test is to categorize the years of OC use to three categories: never, 0-10 years, and >10 years. The second test we categorized the length to 5 categories: never, 0-5 years, 5-10 years, 10-15 years, and >15 years. We found interesting dose-response relationship between the length of years of OC use by PRS for post-menopause women for both sensitivity analysis. We did not observe significant interaction terms for pre-menopause women, the main reason could be not enough power in the analysis as the sample size is small.
data1=array(0,c(6,4))
data1[1,]=fit_normal.coordinate2$res_normal[54,]
data1[2,]=fit_normal.coordinate2$res_normal[55,]
data1[3,]=summary(fit.int.all2)$coef[54,]
data1[4,]=summary(fit.int.all2)$coef[55,]
data1[5,]=fit_normal.coordinate2$res_glm[54,]
data1[6,]=fit_normal.coordinate2$res_glm[55,]
rownames(data1)=c("retro_normal_prs_scaled:factor(oc.cate2)1","prs_scaled:factor(oc.cate2)2","logistic_regression_cohort_prs_scaled:factor(oc.cate2)1","prs_scaled:factor(oc.cate2)2","logistic_regression_casecontrol_prs_scaled:factor(oc.cate2)1","prs_scaled:factor(oc.cate2)2")
colnames(data1)=colnames(fit_normal.coordinate2$res_normal)
data2=array(0,c(12,4))
data2[1:4,]=fit_normal.coordinate3$res_normal[56:59,]
data2[5:8,]=summary(fit.int.all3)$coef[56:59,]
data2[9:12,]=fit_normal.coordinate3$res_glm[56:59,]
rownames(data2)=c(paste0("retro_normal_prs_scaled:factor(oc.cate3)",1:4),paste0("logistic_regression_cohort_prs_scaled:factor(oc.cate3)",1:4),paste0("logistic_regression_casecontrol_prs_scaled:factor(oc.cate3)",1:4))
colnames(data2)=colnames(fit_normal.coordinate3$res_normal)
kable(data1,caption="Sensitivity Analysis 1: PRS X Years of Oral Contraceptive 3 Categories - Post-Menopause Women",digits=4)
Estimate | Std.Error | Z.value | Pvalue | |
---|---|---|---|---|
retro_normal_prs_scaled:factor(oc.cate2)1 | -0.0573 | 0.0606 | -0.9453 | 0.3445 |
prs_scaled:factor(oc.cate2)2 | -0.1487 | 0.0642 | -2.3160 | 0.0206 |
logistic_regression_cohort_prs_scaled:factor(oc.cate2)1 | -0.0875 | 0.0602 | -1.4535 | 0.1461 |
prs_scaled:factor(oc.cate2)2 | -0.1803 | 0.0637 | -2.8306 | 0.0046 |
logistic_regression_casecontrol_prs_scaled:factor(oc.cate2)1 | -0.0539 | 0.0928 | -0.5805 | 0.5616 |
prs_scaled:factor(oc.cate2)2 | -0.1305 | 0.0981 | -1.3301 | 0.1835 |
kable(data2,caption="Sensitivity Analysis 2: PRS X Years of Oral Contraceptive 5 Categories - Post-Menopause Women",digits=4)
Estimate | Std.Error | Z.value | Pvalue | |
---|---|---|---|---|
retro_normal_prs_scaled:factor(oc.cate3)1 | -0.0666 | 0.0694 | -0.9597 | 0.3372 |
retro_normal_prs_scaled:factor(oc.cate3)2 | -0.0476 | 0.0710 | -0.6699 | 0.5029 |
retro_normal_prs_scaled:factor(oc.cate3)3 | -0.1222 | 0.0757 | -1.6141 | 0.1065 |
retro_normal_prs_scaled:factor(oc.cate3)4 | -0.1737 | 0.0748 | -2.3219 | 0.0202 |
logistic_regression_cohort_prs_scaled:factor(oc.cate3)1 | -0.0967 | 0.0688 | -1.4048 | 0.1601 |
logistic_regression_cohort_prs_scaled:factor(oc.cate3)2 | -0.0774 | 0.0704 | -1.0989 | 0.2718 |
logistic_regression_cohort_prs_scaled:factor(oc.cate3)3 | -0.1564 | 0.0751 | -2.0823 | 0.0373 |
logistic_regression_cohort_prs_scaled:factor(oc.cate3)4 | -0.2015 | 0.0738 | -2.7292 | 0.0063 |
logistic_regression_casecontrol_prs_scaled:factor(oc.cate3)1 | -0.0294 | 0.1062 | -0.2770 | 0.7818 |
logistic_regression_casecontrol_prs_scaled:factor(oc.cate3)2 | -0.0786 | 0.1079 | -0.7284 | 0.4663 |
logistic_regression_casecontrol_prs_scaled:factor(oc.cate3)3 | -0.2203 | 0.1162 | -1.8966 | 0.0579 |
logistic_regression_casecontrol_prs_scaled:factor(oc.cate3)4 | -0.0592 | 0.1134 | -0.5222 | 0.6015 |