FindCSE_DEG: Perform CTS-DEG analysis

In WWXkenmo/ENIGMA_test: dEcoNvolutIon method based on reGularized MAtrix completion

Perform CTS-DEG analysis

Description

Analysis the differential expression genes for each cell type

Usage

FindCSE_DEG(
  object,
  y,
  FDR_control = TRUE,
  covariate = NULL,
  FoldChange = FALSE,
  p_cutoff = 0.05
)

Arguments

object	ENIGMA object
FDR_control	if use Wang et al., FDR controlled DEG analysis model. Default: TRUE
covariate	The data.frame object contains the covariate information of each sample
FoldChange	if output the FoldChange of each gene, if FALSE, then output the expression difference
p_cutoff	The pvalue cutoff of gene expression significance test

Value

A list object contain the DEG results of each cell types

Examples

## Not run: 
DEG = FindCSE_DEG(object,y)
DEG = FindCSE_DEG(object,y,covariate=covariate)
head(DEG$celltype1)

## End(Not run)

WWXkenmo/ENIGMA_test documentation built on March 17, 2023, 4:56 a.m.