Retrieve gene set collections from from reactome.db

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

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

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")
#> Error in getReactomeGeneSetDb(species, id.type, rm.species.prefix): User has to provide species approriate org.db to convert reactome id's to ensembl
  gdb.h <- getReactomeGeneSetDb(
    "human",
    id.type = "ensembl",
    org.db = org.Hs.eg.db::org.Hs.eg.db
   )
#> Error in loadNamespace(x): there is no package called ‘org.Hs.eg.db’
 
 gdb.m <- getReactomeGeneSetDb(
    "mouse",
    id.type = "ensembl",
    org.db = org.Mm.eg.db::org.Mm.eg.db
   )
#> Error in loadNamespace(x): there is no package called ‘org.Mm.eg.db’
# }