richGO-ANY-Annot-method: GO Enrichment analysis function

In hurlab/RichR: Function Enrichment analysis and Network construction

GO Enrichment analysis function

Description

GO Enrichment analysis function

Usage

## S4 method for signature 'ANY,Annot'
richGO(
  x,
  godata,
  ontology = "BP",
  pvalue = 0.05,
  padj = NULL,
  minSize = 2,
  maxSize = 500,
  keepRich = TRUE,
  filename = NULL,
  padj.method = "BH",
  sep = ","
)

Arguments

x	vector contains gene names or dataframe with DEGs information
godata	GO annotation data
ontology	BP,MF or CC
pvalue	cutoff pvalue
padj	cutoff p adjust value
minSize	minimal number of genes included in significant terms
maxSize	maximum number of genes included in significant terms
keepRich	keep terms with rich factor value equal 1 or not (default: TRUE)
filename	output filename
padj.method	pvalue adjust method(default:"BH")
sep	character string used to separate the genes when concatenating
organism	organism
keytype	keytype for input genes

Author(s)

Kai Guo

Examples

## Not run: 
  hsago<-buildAnnot(species="human",keytype="SYMBOL",anntype = "GO")
  gene=sample(unique(hsago$GeneID),1000)
  res<-richGO(gene,godata = hsago,ontology ="BP")

## End(Not run)

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