getPantherCollection {sparrow} | R Documentation |
This is a convience function that orchestrates the PANTHER.db package to return GeneSetDb objects for either pathway or GOslim information for human or mouse.
getPantherCollection( type = c("pathway", "goslim"), species = c("human", "mouse") ) getPantherGeneSetDb( type = c("pathway", "goslim"), species = c("human", "mouse") )
type |
"pathway" or, "goslim" |
species |
"human" or "mouse" |
Note that for some reason the PANTHER.db
package needs to be
installed in a user-writable package location for this to work properly.
If you see an error like "Error in resqlite_send_query ... attempt to
write a readonly database", this is the problem. Please install another
version of the PANTHER.db
package in a user-writable directory using
BiocManager::install()
.
A BiocSet of panther pathways
getPantherGeneSetDb
: returns a GeneSetDb
GO Slims are "cut down" versions of the GO ontology that contain a subset of the terms in the whole GO.
PANTHER provides their own set of GO slims, although it's not clear how often these get updated.
# this requires you have the PANTHER.db package installed via BiocManager bsc.panther <- getPantherCollection(species = "human")