clusterProfiler (version 2.0.1)

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)

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

qvalueCutoff

qvalue cutoff

minGSSize

minimal size of genes annotated by Ontology term for testing.

readable

whether mapping gene ID to gene Name

Value

A enrichResult instance.

See Also

enrichResult-class, compareCluster

Examples

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