FindDE: Find DE genes

In xnnba1984/DoubletCollection: Find doublets in scRNA-seq data

Find DE genes

Description

Conduct DE gene analysis on a list of datasets by user-specified methods.

Usage

FindDE(data.removal.list, method.de = "wilcox")

Arguments

data.removal.list	A list of scRNA-seq datasets with cell type annotations.
method.de	A name of DE method: "wilcox", "bimod", "t", "poisson", "negbinom", "LR", or "MAST".

Value

A list of DE gene indices identified for each doublet-detection method.

Examples

table.DE.all <- data.frame()
for(DE.method in c('MAST', 'wilcox', 'bimod')){
 DE.list <- FindDE(data.removal.list = data.removal.list, method.de = DE.method)
 DE.acc.list <- FindDEACC(DE.list=DE.list, DE.truth=data.de$gene.de, gene.all=rownames(data.de$count))
 table.DE <- ListToDataframe(l = DE.acc.list, type = 'barplot')
 table.DE[['DE_method']] <- DE.method
 table.DE.all <- rbind(table.DE.all, table.DE)
}

xnnba1984/DoubletCollection documentation built on Dec. 10, 2022, 11:13 a.m.