richGSEA_internal: Enrichment analysis for any type of annotation data

In guokai8/richR: Function Enrichment analysis and Network construction

Enrichment analysis for any type of annotation data

Description

Enrichment analysis for any type of annotation data

Usage

richGSEA_internal(
  x,
  object,
  keytype = "",
  pvalue = 0.05,
  padj = NULL,
  KEGG = FALSE,
  minSize = 15,
  maxSize = 500,
  minGSSize = 10,
  maxGSSize = 500,
  padj.method = "BH",
  organism = NULL,
  ontology = NULL,
  table = TRUE,
  sep = ","
)

Arguments

x	a vector include all log2FC with gene name
object	annotation file for all genes
pvalue	pvalue cutoff value
padj	adjust p value cut off method
KEGG	a logical evaluating to TRUE or FALSE indicating whether KEGG GSEA were peformed or not.
minSize	Minimal size of a gene set to test. All pathways below the threshold are excluded.
maxSize	Maximal size of a gene set to test. All pathways above the threshold are excluded.
minGSSize	minimal size of genes annotated by ontology term for testing.
maxGSSize	maximal size of each geneset for analyzing
padj.method	p value adjust method
table	leadingEdge as vector
sep	character string used to separate the genes when concatenating

Author(s)

Kai Guo

guokai8/richR documentation built on June 10, 2025, 4:51 a.m.