msigdbr returns the same genesets for mouse as in for human,

Question

[e.r.zakiev]

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:

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

I don't get it

[Jesse]

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?

[e.r.zakiev]

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

[igor]

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

[e.r.zakiev]

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"

[igor]

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.