enrichGSEGOOpt: Estimate enriched GSEA terms using GSEA_internal

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

Estimate enriched GSEA terms using GSEA_internal

Description

Estimate enriched GSEA terms using GSEA_internal

Usage

enrichGSEGOOpt(
  gene.ids,
  org.db,
  organism,
  keyType = "ENTREZID",
  go.environment,
  ont = "BP",
  pvalueCutoff = 1,
  pAdjustMethod = "BH",
  minGSSize = 5,
  maxGSSize = 500,
  readable = FALSE,
  eps = 0,
  exponent = 1,
  seed = FALSE,
  verbose = FALSE,
  ...
)

Arguments

gene.ids	a vector of gene IDs
org.db	organism db, e.g. org.Hs.eg.db::org.Hs.eg.db
organism	Organism, e.g. "Hs"
keyType	(default="ENTREZID")
go.environment	GO environment, see DOSE:::enricher_internal, parameter USER_DATA
ont	type of ontology, one of BP, CC, MF
pvalueCutoff	(default=1)
pAdjustMethod	(default="BH")
minGSSize	(default=5)
maxGSSize	(default=500)
readable	(default=FALSE)
eps	(default=0)
exponent	(default=1)
seed	(default=FALSE)
verbose	Print progress (default=FALSE)
...	additional parameters parsed to DOSE::GSEA_internal

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