enrichKEGG: KEGG Enrichment Analysis of a gene set. Given a vector of...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/enrichKEGG.R

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

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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

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.

use_internal_data

logical, use KEGG.db or latest online KEGG data

Value

A enrichResult instance.

Author(s)

Guangchuang Yu http://guangchuangyu.github.io

See Also

enrichResult-class, compareCluster

Examples

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	data(geneList, package='DOSE')
  de <- names(geneList)[1:100]
	yy <- enrichKEGG(de, pvalueCutoff=0.01)
	head(yy)

clusterProfiler documentation built on Feb. 11, 2021, 2:02 a.m.