knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir="E:/DISC/reproducibility")
utilities_path = "./source/utilities.r"
source(utilities_path)
Registered S3 method overwritten by 'dplyr':
method from
print.rowwise_df
Registered S3 method overwritten by 'htmlwidgets':
method from
print.htmlwidget tools:rstudio
Registered S3 method overwritten by 'data.table':
method from
print.data.table
reldist: Relative Distribution Methods
Version 1.6-6 created on 2016-10-07.
copyright (c) 2003, Mark S. Handcock, University of California-Los Angeles
For citation information, type citation("reldist").
Type help(package="reldist") to get started.
library(limma)
method_name = c("Raw", "DISC", "scVI", "MAGIC", "DCA", "scScope", "DeepImpute", "VIPER", "scImpute")
method_color = c("#A5A5A5", "#E83828", "#278BC4", "#EADE36", "#198B41", "#920783", "#F8B62D", "#8E5E32", "#1E2B68")
text_color = rep("black", length(method_name))
names(text_color) = method_name
text_color["DISC"] = "red"
options(future.globals.maxSize= 4.5e9)
gene_bulk_mat = readh5_loom("./data/JURKAT_293T/bulk.loom")
[1] "./data/JURKAT_293T/bulk.loom"
[1] 58011 4
gene_bulk_filt0 = round(gene_bulk_mat[!grepl('^MT-', rownames(gene_bulk_mat)), ])
gene_bulk_filt1 = gene_bulk_filt0[rowSums(gene_bulk_filt0 > 0) > 0, ]
bulk_sample_cell_type = sapply(colnames(gene_bulk_filt1), function(x){
return(strsplit(x, "_", fixed = T)[[1]][[2]])
})
design_mat = cbind(1, ifelse(bulk_sample_cell_type == bulk_sample_cell_type[1], 1, 0))
fit <- eBayes(lmFit(voom(gene_bulk_filt1, design = design_mat), design = design_mat))
bulk_DE_matrix = topTable(fit, coef = 2, number = nrow(gene_bulk_filt1))
bulk_DEG = rownames(bulk_DE_matrix)[abs(bulk_DE_matrix[, "logFC"]) >= 1.5 & bulk_DE_matrix[, "adj.P.Val"] <= 0.05]
print(head(bulk_DE_matrix))
print(head(bulk_DEG))
[1] "XIST" "TMSB4X" "BCL11B" "TCF7" "NEFM" "PRKCB"
if(!file.exists("./results/JURKAT_293T/sc_DEG_list.rds")){
dir.create("./results/JURKAT_293T", showWarnings = F, recursive = T)
gene_bc_mat = readh5_loom("./data/JURKAT_293T/raw.loom")
cell_293T = colnames(gene_bc_mat)[grep("293T", colnames(gene_bc_mat))]
cell_Jurkat = colnames(gene_bc_mat)[grep("JURKAT", colnames(gene_bc_mat))]
cell_type = c(rep("293T", length(cell_293T)), rep("Jurkat", length(cell_Jurkat)))
names(cell_type) = c(cell_293T, cell_Jurkat)
cell_type = cell_type[colnames(gene_bc_mat)]
cell_type = factor(cell_type, levels = sort(unique(cell_type)))
gene_filter = gene_selection(gene_bc_mat, 10)
sc_gene = rownames(gene_bc_mat)[gene_filter]
sc_DEG_list = list(wilcox = list(), MAST = list())
for(ii in method_name){
if(ii == "Raw"){
gene_bc_filt = gene_bc_mat[sc_gene, ]
}else{
gene_bc_mat = readh5_loom(paste0("./data/JURKAT_293T/", ii, "_JURKAT_293T.loom"))
gene_bc_filt = gene_bc_mat[sc_gene, ]
}
seurat_obj = CreateSeuratObject(counts = as.data.frame(gene_bc_filt), min.cells = 0, min.features = 0)
seurat_obj = NormalizeData(seurat_obj, normalization.method = "LogNormalize", scale.factor = 10000)
seurat_obj@active.ident = cell_type
suppressWarnings({sc_DEG_list[["wilcox"]][[ii]] = FindMarkers(seurat_obj, ident.1 = "293T", ident.2 = "Jurkat", min.pct = 0.1, logfc.threshold = 0, test.use = "wilcox", verbose = F)})
suppressWarnings({sc_DEG_list[["MAST"]][[ii]] = FindMarkers(seurat_obj, ident.1 = "293T", ident.2 = "Jurkat", min.pct = 0.1, logfc.threshold = 0, test.use = "MAST", verbose = F)})
print(ii)
}
saveRDS(sc_DEG_list, paste0("./results/JURKAT_293T/sc_DEG_list.rds"))
}else{
sc_DEG_list = readRDS(paste0("./results/JURKAT_293T/sc_DEG_list.rds"))
}
[1] "./data/JURKAT_293T/raw.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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[1] "Raw"
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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Done!
[1] "DISC"
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "scVI"
[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "MAGIC"
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
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Refitting on reduced model...
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Done!
[1] "DCA"
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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Done!
[1] "scScope"
[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "DeepImpute"
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "VIPER"
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "scImpute"
if(!file.exists("./results/JURKAT_293T/sc_false_DEG_list.rds")){
dir.create("./results/JURKAT_293T", showWarnings = F, recursive = T)
gene_bc_mat = readh5_loom("./data/JURKAT_293T/raw.loom")
gene_filter = gene_selection(gene_bc_mat, 10)
sc_gene = rownames(gene_bc_mat)[gene_filter]
cell_293T = colnames(gene_bc_mat)[grep("293T", colnames(gene_bc_mat))]
df = expand.grid(c(10, 50, 100, 500), c(10, 50, 100, 500))
colnames(df) = c("n1", "n2")
df = df[df[, "n1"] <= df[, "n2"], ]
sc_false_DEG_list = list(wilcox = list(), MAST = list())
for(ii in seq(nrow(df))){
cn1 = df[ii, "n1"]
cn2 = df[ii, "n2"]
set.seed(12345)
id = sample(seq(length(cell_293T)), cn1 + cn2)
this_name = paste0(cn1, '_', cn2)
for(jj in method_name){
if(jj == "Raw"){
expr = gene_bc_mat[sc_gene, cell_293T][, id]
}else{
gene_bc_mat = readh5_loom(paste0("./data/JURKAT_293T/", jj, "_JURKAT_293T.loom"))
expr = gene_bc_mat[sc_gene, cell_293T][, id]
}
if(jj == method_name[1]){
sc_false_DEG_list[["wilcox"]][[jj]] = list()
sc_false_DEG_list[["MAST"]][[jj]] = list()
}
seurat_obj = CreateSeuratObject(counts = as.data.frame(expr), min.cells = 0, min.features = 0)
seurat_obj = NormalizeData(seurat_obj, normalization.method = "LogNormalize", scale.factor = 10000)
cell_type = c(rep("cn1", cn1),rep("cn2", cn2))
names(cell_type) = colnames(expr)
seurat_obj@active.ident = factor(cell_type, levels = sort(unique(cell_type)))
suppressWarnings({sc_false_DEG_list[["wilcox"]][[jj]][[this_name]] = FindMarkers(seurat_obj, ident.1 = "cn1", ident.2 = "cn2", min.pct = 0.1, logfc.threshold = 0, test.use = "wilcox", verbose = F)})
suppressWarnings({sc_false_DEG_list[["MAST"]][[jj]][[this_name]] = FindMarkers(seurat_obj, ident.1 = "cn1", ident.2 = "cn2", min.pct = 0.1, logfc.threshold = 0, test.use = "MAST", verbose = F)})
}
print(this_name)
}
saveRDS(sc_false_DEG_list, paste0("./results/JURKAT_293T/sc_false_DEG_list.rds"))
}else{
sc_false_DEG_list = readRDS(paste0("./results/JURKAT_293T/sc_false_DEG_list.rds"))
}
[1] "./data/JURKAT_293T/raw.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "10_10"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
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Refitting on reduced model...
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[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Combining coefficients and standard errors
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Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "10_50"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "50_50"
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Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "10_100"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Combining coefficients and standard errors
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "50_100"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "100_100"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Combining coefficients and standard errors
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
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Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "10_500"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "50_500"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
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Refitting on reduced model...
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[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
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Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "100_500"
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Combining coefficients and standard errors
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DISC_JURKAT_293T.loom"
[1] 32738 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/scVI_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/MAGIC_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
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**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/DCA_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
[1] "./data/JURKAT_293T/scScope_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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[1] "./data/JURKAT_293T/DeepImpute_JURKAT_293T.loom"
[1] 13328 6143
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Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/VIPER_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Refitting on reduced model...
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Done!
[1] "./data/JURKAT_293T/scImpute_JURKAT_293T.loom"
[1] 13328 6143
Feature names cannot have underscores ('_'), replacing with dashes ('-')Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Assuming data assay in position 1, with name et is log-transformed.
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Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...
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Done!
[1] "500_500"
overlap_wilcox = sapply(sc_DEG_list[["wilcox"]], function(x){
return(mean(sapply(seq(100) * 10, function(y){
return(mean(rownames(x[order(x[, "p_val_adj"]), ])[seq(y)] %in% bulk_DEG))
})))
})
overlap_MAST = sapply(sc_DEG_list[["MAST"]], function(x){
return(mean(sapply(seq(100) * 10, function(y){
return(mean(rownames(x)[seq(y)] %in% bulk_DEG))
})))
})
print(overlap_MAST)
Raw DISC scVI MAGIC DCA scScope DeepImpute VIPER scImpute
0.6084401 0.6891465 0.5364339 0.4615233 0.5467916 0.6190999 0.5231432 0.5919032 0.6029579
print(overlap_wilcox)
Raw DISC scVI MAGIC DCA scScope DeepImpute VIPER scImpute
0.5883429 0.6877088 0.5364339 0.4615233 0.5467488 0.5944116 0.4874671 0.5759028 0.5910734
Note: This result has tiny difference from our paper as the sample cell is different.
DEG_wilcox_false = sapply(sc_false_DEG_list[["wilcox"]], function(x){
return(sapply(x, function(y){
return(sum(y[, "p_val"] <= 0.01 & abs(y[, "avg_logFC"]) >= 0.25))
}))
})
wilcox_false_mean = colMeans(DEG_wilcox_false)
print(wilcox_false_mean)
Raw DISC scVI MAGIC DCA scScope DeepImpute VIPER scImpute
21.7 4.8 0.0 0.0 0.0 18.7 10.4 12.6 11.3
DEG_MAST_false = sapply(sc_false_DEG_list[["MAST"]], function(x){
return(sapply(x, function(y){
return(sum(y[, "p_val"] <= 0.01 & abs(y[, "avg_logFC"]) >= 0.25))
}))
})
MAST_false_mean = colMeans(DEG_MAST_false)
print(MAST_false_mean)
Raw DISC scVI MAGIC DCA scScope DeepImpute VIPER scImpute
18.7 2.4 0.0 0.0 0.0 20.8 9.9 12.1 9.9
plot_df = data.frame(omo = (1 - overlap_wilcox[method_name]), fm = wilcox_false_mean[method_name], method = method_name)
ggplot(plot_df, aes(x = fm, y = omo, label = method, color = method)) + geom_point() + geom_text_repel() + theme_bw() + theme(legend.position = "none") + xlab("False DEG (293T)") + ylab("1 - Overlap") + ggtitle("wilcox") + scale_colour_manual(values = method_color)
plot_df = data.frame(omo = (1 - overlap_MAST[method_name]), fm = MAST_false_mean[method_name], method = method_name)
ggplot(plot_df, aes(x = fm, y = omo, label = method, color = method)) + geom_point() + geom_text_repel() + theme_bw() + theme(legend.position = "none") + xlab("False DEG (293T)") + ylab("1 - Overlap") + ggtitle("MAST") + scale_colour_manual(values = method_color)