enrichGO2: GO Term Enrichment with Hypergeometric Test

View source: R/oraAnalyzer.R

enrichGO2R 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 ontology should be combined

Value

A feaResult instance.

See Also

feaResult-class

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))

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.