llrs/BioCor

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