Allow to convert pathway information to GeneSetCollection
Closed this issue · 1 comments
llrs commented
Related to #3, instead of using lists from metabolic pathways databases, use GeneSetCollections
library("reactome.db")
genesReact <- as.list(reactomeEXTID2PATHID)
It would be great to work with:
library("reactome.db")
genesReact <- as.GeneSetCollection(reactomeEXTID2PATHID)
genesReact
## GeneSetCollection
## names: R-HSA-109582, R-HSA-114608, R-HSA-168249, R-HSA-168256, R-HSA-6798695, R-HSA-76002, ... (22001 total)
## unique identifiers: 5167, 100288400, ..., 57191 (69713 total)
## types in collection:
## geneIdType: EntrezIdentifier (1 total)
llrs commented
library("reactome.db")
genesReact <- as.GeneSetCollection(as.list(reactomeEXTID2PATHID))
genesReact
## GeneSetCollection
## names: R-ATH-109581, R-ATH-109582, ..., R-XTR-997272 (22001 total)
## unique identifiers: 820753, 826595, ..., 100498135 (69713 total)
## types in collection:
## geneIdType: NullIdentifier (1 total)
## collectionType: NullCollection (1 total)
Since 76831b5