richGSEA-ANY-Annot-method: GSEA Enrichment analysis function

In hurlab/RichR: Function Enrichment analysis and Network construction

GSEA Enrichment analysis function

Description

GSEA Enrichment analysis function

Usage

## S4 method for signature 'ANY,Annot'
richGSEA(
  x,
  object,
  keytype = "",
  pvalue = 0.05,
  padj = NULL,
  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
pvalue	pvalue cutoff value
padj	adjust p value cut off method
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	p value adjust method
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")
name=sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene)<-name
res<-richGSEA(gene,object = hsako)

## End(Not run)

hurlab/RichR documentation built on Feb. 5, 2024, 8:07 p.m.