R: GO Term Enrichment with Hypergeometric Test

enrichGO2 {signatureSearch}

R Documentation

GO Term Enrichment with Hypergeometric Test

Description

Given a vector of gene identifiers, this function returns GO term enrichment results based on a hypergeometric test with duplication support in the test set.

Usage

enrichGO2(
  gene,
  OrgDb,
  keytype = "SYMBOL",
  ont = "MF",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  qvalueCutoff = 0.2,
  minGSSize = 5,
  maxGSSize = 500,
  pool = FALSE
)

Arguments

`gene`	a vector of gene SYMBOL ids (here the test set)
`OrgDb`	OrgDb
`keytype`	Gene ID type of test set
`ont`	One of "MF", "BP", "CC" or "ALL"
`pvalueCutoff`	pvalue cutoff
`pAdjustMethod`	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`universe`	background genes
`qvalueCutoff`	qvalue cutoff
`minGSSize`	minimum size of each gene set in annotation system
`maxGSSize`	maximum size of each gene set in annotation system
`pool`	If ont='ALL', whether 3 GO ontologies should be combined

Value

A feaResult instance.

Examples

# The method supports duplicated elements in 'gene', 
# which should be gene SYMBOL ids for GO term enrichment.
gene <- c(rep("HDAC1",4), rep("HDAC3",2), "SOX8", "KLK14")
# data(targetList)
# ego <- enrichGO2(gene = gene, OrgDb="org.Hs.eg.db", ont="MF",
#                  universe=names(targetList))