enrichGOOpt: Enrich gene ontologies using enricher_internal

In kharchenkolab/cacoa: Case-Control Analysis Tools for Single-Cell RNA-Seq

Enrich gene ontologies using enricher_internal

Description

Enrich gene ontologies using enricher_internal

Usage

enrichGOOpt(
  gene,
  org.db,
  go.environment,
  keyType = "ENTREZID",
  ont = "BP",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe = NULL,
  qvalueCutoff = 0.2,
  minGSSize = 5,
  maxGSSize = 500,
  readable = FALSE
)

Arguments

gene	a vector of entrez gene IDs
org.db	organism db, e.g. org.Hs.eg.db::org.Hs.eg.db
go.environment	GO environment, see DOSE:::enricher_internal, parameter USER_DATA
keyType	Gene key type (default="ENTREZID")
ont	type of ontology, one of BP, CC, or MF (default="BP")
readable	See DOSE:::enricher_internal (default=FALSE)

kharchenkolab/cacoa documentation built on Nov. 8, 2024, 6:06 a.m.