DEGeneModules: Filter gene modules based on differential expression...

In alexthiery/scHelper: R package containing helper functions for single cell analysis

Filter gene modules based on differential expression (seurat::FindAllMarkers)

Description

Filter gene modules based on differential expression (seurat::FindAllMarkers)

Usage

DEGeneModules(
  seurat_data,
  gene_modules,
  logfc = 0.25,
  pval = 0.001,
  selected_gene_proportion = 0.5,
  active_ident = NULL
)

Arguments

gene_modules	named list of gene modules
logfc	logFC cutoff used for differential expression
pval	adjusted pvalue
selected_gene_proportion	proportion of genes in gene module which are required to pass differential expression test
active_ident	column in @meta.data which is to be used as the groupings for differential expression testing
seurat_object	Seurat object

Value

gene module list

alexthiery/scHelper documentation built on Aug. 26, 2023, 3:42 p.m.