msigdbr returns the same genesets for mouse as in for human,
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14 months ago
e.r.zakiev ▴ 210

If we were to query the MSigDb database for mouse and human, respectively:

mauz <-msigdbr::msigdbr(species = 'Mus musculus')
hooman <-msigdbr::msigdbr(species = "Homo sapiens")

And counted the number of genesets from the C8 category, for instance, then both queries would yield the same number of 700 genesets:

nrow(unique(mauz[mauz[,1]=="C8",3]))

700

nrow(unique(hooman[hooman[,1]=="C8",3]))

700

And if for the human that is more or less close to the expected value, according to MSigDB's website:

enter image description here

for the mouse that number should be close or equal to 232

enter image description here

I don't get it

msigdbr • 1.4k views
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It looks like that function goes out of its way to get orthologs from the human genome and merge them into the returned info. Could that explain what you see?

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yes, it looks like you are right. Would be nice to have a way to query the mouse-specific genesets only :(

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0
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You are asking for C8 In the code, but you show M8 in the screenshot.

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hello Igor, thanks for the great package. How do I query for mouse sets?

msigdbr::msigdbr(species = "Mus musculus", category = "M8")

returns an error "unknown category"

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The addition of mouse-specific pathways to MSigDB is relatively recent. The package has not been updated to incorporate the latest version of the database.

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