richKEGG-ANY-Annot-method: KEGG Enrichment analysis function

In hurlab/RichR: Function Enrichment analysis and Network construction

KEGG Enrichment analysis function

Description

KEGG Enrichment analysis function

Usage

## S4 method for signature 'ANY,Annot'
richKEGG(
  x,
  kodata,
  pvalue = 0.05,
  padj = NULL,
  organism = NULL,
  ontology = "KEGG",
  keytype = NULL,
  minSize = 2,
  maxSize = 500,
  keepRich = TRUE,
  filename = NULL,
  padj.method = "BH",
  builtin = TRUE,
  sep = ","
)

Arguments

x	vector contains gene names or dataframe with DEGs information
pvalue	cutoff pvalue
padj	cutoff p adjust value
organism	organism
ontology	KEGG
keytype	keytype for input genes
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
bulitin	use KEGG bulit in KEGG annotation or not(set FALSE if you want use newest KEGG data)

Author(s)

Kai Guo

Examples

## Not run: 
  hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
  gene=sample(unique(hsako$GeneID),1000)
  res<-richKEGG(gene,kodata = hsako)

## End(Not run)

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