enrichGO: GO Enrichment Analysis of a gene set. Given a vector of...

In aiminy/ModifiedclusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters

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

An enrichResult instance.

Author(s)

Guangchuang Yu http://ygc.name

See Also

enrichResult-class, compareCluster

Examples

## 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)

aiminy/ModifiedclusterProfiler documentation built on May 10, 2019, 7:37 a.m.