msigdbr returns the same genesets for mouse as in for human,
0
0
Entering edit mode
20 months ago
e.r.zakiev ▴ 230

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 • 1.6k views
ADD COMMENT
2
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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"

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2058 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6