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

Source: R/enhance_enrichGO.R

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

enhance_enrichGO(
  gene,
  OrgDb,
  keyType = "ENTREZID",
  ont = "MF",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500,
  readable = FALSE,
  pool = FALSE,
  simplify = FALSE
)

Arguments

gene

a vector of entrez gene id.

OrgDb

OrgDb

keyType

keytype of input gene

ont

One of "BP", "MF", and "CC" subontologies, or "ALL" for all three.

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.

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.

minGSSize

minimal size of genes annotated by Ontology term for testing.

maxGSSize

maximal size of genes annotated for testing

readable

whether mapping gene ID to gene Name

pool

If ont='ALL', whether pool 3 GO sub-ontologies

simplify

whether simplify

Value

An enrichResult instance.

See also

enrichResult-class, compareCluster

Author

Guangchuang Yu https://guangchuangyu.github.io

Examples

if (FALSE) {
  data(geneList, package = "DOSE")
  de <- names(geneList)[1:100]
  yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
  head(yy)
}