enrichKEGG: KEGG 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

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.

Author(s)

Guangchuang Yu http://ygc.name

See Also

enrichResult-class, compareCluster

Examples

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

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