goEnrichment: goEnrichment

In demuellae/muRtools: Mueller's R tools

goEnrichment

Description

Perform Gene Ontology (GO) enrichment using the topGO package

Usage

goEnrichment(
  qids,
  uids,
  ontology = "BP",
  idType = "ensembl",
  assembly = "org.Hs.eg.db",
  algorithm = "weight01"
)

Arguments

qids	character vector of query gene IDs
uids	character vector of universe gene IDs
ontology	character specifying the ontology to use (default: "BP")
idType	character specifying which universe the gene IDs come from (default: "ensembl"). Possible values are: "entrez", "genbank", "alias", "ensembl", "symbol", "genename", "unigene"
assembly	character specifying the genome to use. Can either be the name of the package to be used for mapping the identifiers (e.g. "org.Hs.eg.db"; default) or an identifier for a genome assembly ((e.g. "hg38")
algorithm	algorithm employed by topGO. See topgGO::runTest for details.

Value

a list (S3 class) object containing: - $tgData: the used topGOdata object - $resultObj: the resulting topGOresult object - $table: a summary table of statistics for each GO term

Author(s)

Fabian Mueller

demuellae/muRtools documentation built on Nov. 6, 2024, 9:44 a.m.