clusterProfiler (version 3.0.4)

enrichKEGG: KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.

Description

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

Usage

enrichKEGG(gene, organism = "hsa", keyType = "kegg", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500, qvalueCutoff = 0.2, use_internal_data = FALSE)

Arguments

gene

a vector of entrez gene id.

organism

supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html'

keyType

one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'

pvalueCutoff

Cutoff value of pvalue.

pAdjustMethod

one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"

universe

background genes

minGSSize

minimal size of genes annotated by Ontology term for testing.

maxGSSize

maximal size of genes annotated for testing

qvalueCutoff

qvalue cutoff

use_internal_data

logical, use KEGG.db or latest online KEGG data

Value

A enrichResult instance.

See Also

enrichResult-class, compareCluster

Examples

	data(gcSample)
	yy = enrichKEGG(gcSample[[5]], pvalueCutoff=0.01)
	head(summary(yy))
	#plot(yy)