clusterProfiler: enrichMKEGG – R documentation

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enrichMKEGG

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.

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

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`	adjusted pvalue cutoff on enrichment tests to report
`pAdjustMethod`	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`universe`	background genes. If missing, the all genes listed in the database (eg TERM2GENE table) will be used as background.
`minGSSize`	minimal size of genes annotated by Ontology term for testing.
`maxGSSize`	maximal size of genes annotated for testing
`qvalueCutoff`	qvalue cutoff on enrichment tests to report as significant. Tests must pass i) `pvalueCutoff` on unadjusted pvalues, ii) `pvalueCutoff` on adjusted pvalues and iii) `qvalueCutoff` on qvalues to be reported.

Value

A enrichResult instance.

clusterProfiler

statistical analysis and visualization of functional profiles for genes and gene clusters

v3.18.1

Artistic-2.0

Authors

Guangchuang Yu [aut, cre, cph] (<https://orcid.org/0000-0002-6485-8781>), Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)

Initial release