enrich_internal: Enrichment analysis for any type of annotation data
In guokai8/richR: Function Enrichment analysis and Network construction

enrich_internal

R Documentation

Enrichment analysis for any type of annotation data

Description

Enrichment analysis for any type of annotation data

Usage

enrich_internal(
  x,
  object,
  ontology = "",
  pvalue = 0.05,
  padj = NULL,
  organism = NULL,
  minSize = 1,
  maxSize = 500,
  minGSSize = 10,
  maxGSSize = 500,
  keepRich = TRUE,
  keytype = "",
  filename = NULL,
  padj.method = "BH",
  sep = ","
)

Arguments

`x`	vector contains gene names or dataframe with DEGs information
`object`	annotation data
`ontology`	ontology type
`pvalue`	cutoff pvalue
`padj`	cutoff p adjust value
`organism`	organism
`minSize`	minimal number of genes included in significant terms
`maxSize`	maximum number of genes included in significant terms
`minGSSize`	minimal size of genes annotated by ontology term for testing.
`maxGSSize`	maximal size of each geneset for analyzing
`keepRich`	keep terms with rich factor value equal 1 or not (default: TRUE)
`keytype`	keytype for input genes
`filename`	output filename
`padj.method`	pvalue adjust method(default:"BH")
`sep`	character string used to separate the genes when concatenating