Learn R Programming

clusterProfiler (version 3.0.4)

enrichGO: GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.

Description

GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.

Usage

enrichGO(gene, OrgDb, keytype = "ENTREZID", ont = "MF", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500, readable = FALSE)

Arguments

gene
a vector of entrez gene id.
OrgDb
OrgDb
keytype
keytype of input gene
ont
One of "MF", "BP", and "CC" subontologies.
pvalueCutoff
Cutoff value of pvalue.
pAdjustMethod
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe
background genes
qvalueCutoff
qvalue cutoff
minGSSize
minimal size of genes annotated by Ontology term for testing.
maxGSSize
maximal size of genes annotated for testing
readable
whether mapping gene ID to gene Name

Value

A enrichResult instance.

See Also

enrichResult-class, compareCluster

Examples

Run this code
## Not run: 
# 	data(gcSample)
# 	yy <- enrichGO(gcSample[[1]], 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
# 	head(summary(yy))
# 	plot(yy)
# ## End(Not run)

Run the code above in your browser using DataLab