enrichGO2: GO Term Enrichment with Hypergeometric Test

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

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.