richGSEA-ANY-data.frame-method: GSEA Enrichment analysis function

richGSEA,ANY,data.frame-methodR Documentation

GSEA Enrichment analysis function

Description

GSEA Enrichment analysis function

Usage

## S4 method for signature 'ANY,data.frame'
richGSEA(
  x,
  object,
  keytype = "",
  pvalue = 0.05,
  padj = NULL,
  KEGG = FALSE,
  minSize = 15,
  ontology = ontology,
  maxSize = 500,
  padj.method = "BH",
  organism = NULL,
  table = TRUE,
  sep = ","
)

Arguments

x

a vector include all log2FC with gene name

object

annotation file for all genes

keytype

keytype for input 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.

padj.method

pvalue adjust method(default:"BH")

organism

organism name

table

leadingEdge as vector

sep

character string used to separate the genes when concatenating

Author(s)

Kai Guo

Examples

## Not run: 
hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
hsako<-as.data.frame(hsako)
name=sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene)<-name
res<-richGSEA(gene,object = hsako)

## End(Not run)

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