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

In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

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 = "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 'https://www.genome.jp/kegg/catalog/org_list.html'
keyType	one of "kegg", 'ncbi-geneid', 'ncbi-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 https://yulab-smu.top

See Also

enrichResult-class, compareCluster

Examples

## Not run: 
  data(geneList, package='DOSE')
  de <- names(geneList)[1:100]
  yy <- enrichKEGG(de, pvalueCutoff=0.01)
  head(yy)

## End(Not run)

YuLab-SMU/clusterProfiler documentation built on Dec. 3, 2024, 1:32 p.m.