Closed lianos closed 3 years ago
The getMSigGeneSetDb function updated to use msigdbr, and the msigdb.data package has been dropped as a dependency.
getMSigGeneSetDb
The functionality provided is still roughly the same, but promotion of subcategories to main collections is a bit different:
promote_subcategory_to_collection
FALSE
"kegg"
"go"
"MSigDB_"
prefix_collection = TRUE
The implementation of scale_rows has changed a bit. Be very weary of setting scale = TRUE when normalizing against a subset of samples.
scale_rows
scale = TRUE
The
getMSigGeneSetDb
function updated to use msigdbr, and the msigdb.data package has been dropped as a dependency.The functionality provided is still roughly the same, but promotion of subcategories to main collections is a bit different:
promote_subcategory_to_collection
is nowFALSE
"kegg"
or"go"
as main collections (for now)"MSigDB_"
withprefix_collection = TRUE
The implementation of
scale_rows
has changed a bit. Be very weary of settingscale = TRUE
when normalizing against a subset of samples.