richKEGG_internal: KEGG Pathway Enrichment analysis function
In hurlab/RichR: Function Enrichment analysis and Network construction

richKEGG_internal

R Documentation

KEGG Pathway Enrichment analysis function

Description

KEGG Pathway Enrichment analysis function

Usage

richKEGG_internal(
  x,
  kodata,
  pvalue = 0.05,
  padj = NULL,
  ontology = "KEGG",
  organism = NULL,
  keytype = "SYMBOL",
  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
`kodata`	GO annotation data
`pvalue`	cutoff pvalue
`padj`	cutoff p adjust value
`ontology`	KEGG
`organism`	organism
`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)