getReactomeCollection: Retrieve gene set collections from from reactome.db

In lianos/sparrow: Take command of set enrichment analyses through a unified interface

Retrieve gene set collections from from reactome.db

Description

Retrieve gene set collections from from reactome.db

Usage

getReactomeCollection(
  species = "human",
  id.type = c("entrez", "ensembl"),
  rm.species.prefix = TRUE
)

getReactomeGeneSetDb(
  species = "human",
  id.type = c("entrez", "ensembl"),
  rm.species.prefix = TRUE
)

Arguments

species	the species to get pathay information for
id.type	"entrez" or "ensembl"
rm.species.prefix	pathways are provided with species prefixes from reactome.db, when TRUE (default), these are stripped from the gene set names.

Value

a reactome BiocSet object

Functions

• getReactomeGeneSetDb(): returns a GeneSetDb object

Examples

  bsc.h <- getReactomeCollection("human")
  gdb.h <- getReactomeGeneSetDb("human")

lianos/sparrow documentation built on Feb. 5, 2024, 2:58 p.m.