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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/enrichGO.R

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

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

pool

If ont='ALL', whether pool 3 GO sub-ontologies

Value

An enrichResult instance.

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

See Also

enrichResult-class, compareCluster

Examples

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## Not run: 
    data(geneList)
	de <- names(geneList)[1:100]
	yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
	head(yy)

## End(Not run)

Bioconductor-mirror/clusterProfiler documentation built on July 28, 2017, 5:21 a.m.