clusterProfiler (version 2.4.1)

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 = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 5, qvalueCutoff = 0.2, readable = FALSE, use_internal_data = FALSE)

Arguments

gene

a vector of entrez gene id.

organism

One of "anopheles", "arabidopsis", "bovine", "canine", "chicken", "chimp", "ecolik12","ecsakai", "fly", "human", "malaria", "mouse", "pig", "rat","rhesus", "worm", "xenopus", "yeast" and "zebrafish".

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.

qvalueCutoff

qvalue cutoff

readable

whether mapping gene ID to gene Name

use_internal_data

logical, if TRUE, use KEGG.db. default is FALSE, will download 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)