richGO-methods: richGO method

In hurlab/RichR: Function Enrichment analysis and Network construction

richGO method

Description

richGO

Usage

richGO(
  x,
  godata,
  ontology = "BP",
  pvalue = 0.05,
  padj = NULL,
  organism = NULL,
  keytype = 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
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

Value

richResult

Author(s)

Kai Guo

Examples

## Not run: 
hsago <- buildAnnot(species="human",keytype="SYMBOL",anntype = "GO")
hsago <- as.data.frame(hsago)
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.