Entering edit mode
11 weeks ago
e.r.zakiev ▴ 50
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:
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
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?
yes, it looks like you are right. Would be nice to have a way to query the mouse-specific genesets only :(
You are asking for C8 In the code, but you show M8 in the screenshot.
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"
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.