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msigdb Collection C4 subcategory 3CA unknown #41

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csmoreno opened this issue Nov 9, 2024 · 0 comments

csmoreno commented Nov 9, 2024

I was trying to use msigdbr for the C4_3CA collection and I get this error:

Computational_pathwaysDF <- msigdbr("human", category="C4",subcategory = "3CA")
Error in msigdbr("human", category = "C4", subcategory = "3CA") :
unknown subcategory

When I print out the collections

print(msigdbr_collections(),n=30)
I get this
...
12 C3 "TFT:TFT_Legacy" 610
13 C4 "CGN" 427
14 C4 "CM" 431
15 C5 "GO:BP" 7658
...

I was able to download the C4 3CA collection here:
https://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2024.1.Hs/c4.3ca.v2024.1.Hs.json
but it is in a different format than the dataframe format provided by msigdbr.

Is there a way to import the json file into msigdbr or to convert it into the dataframe format from the list format in the json file?

Thanks

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