Retrieve gene set collections from from reactome.db

Retrieve gene set collections from from reactome.db

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

# \donttest{
  bsc.h <- getReactomeCollection("human")
  gdb.h <- getReactomeGeneSetDb("human")
#> Error in getReactomeGeneSetDb("human"): could not find function "getReactomeGeneSetDb"
# }