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montilab / hypeR

An R Package for Geneset Enrichment Workflows
https://montilab.github.io/hypeR-docs/
GNU General Public License v3.0
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msigdb_gsets doesn't give me all the CP gene sets #13

Closed gungorbudak closed 4 years ago

gungorbudak commented 4 years ago

Hi,

I just reinstalled hypeR from its GitHub master branch and tried following to obtain canonical pathways from MSigDB:

CP <- msigdb_gsets("Homo sapiens", "C2", "CP")

With this, I'm expecting to get 2199 gene sets including BIOCARTA, KEGG, PID, REACTOME and more listed here: http://software.broadinstitute.org/gsea/msigdb/collection_details.jsp#CP But instead it returns an object with 29 gene sets.

length(CP$genesets)
[1] 29

Any idea why this would happen? Is this something caused by msigdbr?

Thanks much!

anfederico commented 4 years ago

hypeR wraps around the msigdbr package. It seems as though you cannot request the CP pathways like this, otherwise it would (or should) work in hypeR. I'd pull those genesets with msigdb_download() independently and just merge them.

igordot commented 4 years ago

If anyone is curious, some clarification about the number of retrieved gene sets can be found here: https://github.com/igordot/msigdbr/issues/4