enrichMKEGG: KEGG Module Enrichment Analysis of a gene set. Given a vector...

Description Usage Arguments Value

View source: R/enrichMKEGG.R

Description

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

Usage

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

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

Value

A enrichResult instance.


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