enrich: enrich method

In guokai8/richR: Function Enrichment analysis and Network construction

enrich method

Description

enrich

Usage

enrich(
  x,
  object,
  ontology = "",
  pvalue = 0.05,
  padj = NULL,
  organism = NULL,
  keytype = "",
  filename = NULL,
  minSize = 2,
  maxSize = 500,
  minGSSize = 10,
  maxGSSize = 500,
  keepRich = TRUE,
  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
keytype	keytype for input genes
filename	output filename
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)
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: 
library(bioAnno)
fromKEGG(species="ath")
athgo <- buildOwn(dbname="org.ath.eg.db",anntype="GO")
athgo <- as.data.frame(athgo)
athgo <- na.omit(athgo)
gene <- sample(unique(athgo$GeneID),1000)
res <- enrich(gene,athgo)

## End(Not run)

guokai8/richR documentation built on June 10, 2025, 4:51 a.m.