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martinjzhang / scDRS

Single-cell disease relevance score (scDRS)
https://martinjzhang.github.io/scDRS/
MIT License
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fail to get the "1000 top associated genes" based on MAGMA #93

Closed yihancc closed 1 month ago

yihancc commented 1 month ago

Hi, thans for this wonderful tool!

I would like to generate .gs files for other diseases that are not in your article. Based on MAGMA, I used the association statistics from GWAS just as you suggested https://github.com/martinjzhang/scDRS/issues/89 , but finally got only 59 genes for one disease instead of 1000 genes.

I am worried that such a small number of genes will seriously affect my results. Could you please give me some advice on how to generate the "1000 most associated genes" based on MAGMA?

Thank you very much!

martinjzhang commented 1 month ago

59 genes should work. We have used genesets with 10-20 genes in the paper. For generating "1000 most associated genes", you will need genomewide association statistics. See instructions here: https://github.com/martinjzhang/scDRS/issues/2

yihancc commented 1 month ago

Thank you so much for your reply! I will have a try.