Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PascalX doesn't score genes when rsid is the last column in the GWAS sumstats file #37

Open
mjbeyeler opened this issue Apr 14, 2024 · 0 comments
Labels
bug Something isn't working

Comments

@mjbeyeler
Copy link
Member

Hi,

I think I discovered a bug when loading GWAS sumstats. Some of my sumstats have the rsid as the last column in the file. This resulted in seemingly correct loading of the data. PascalX proceeds to scoring the genes, but the scoring results in 0 genes scored.

After some trial and error, I realized that simply putting the rsid column not as the last one solved the issue.

As a minimal example, this was the format of the .tsv that worked:

rsid	Effect	P-value
rs7899632	-0.0246	0.0958

This is the same file, with rsid as the last column, that doesn't work:

Effect	P-value	rsid
-0.0246	0.0958	rs7899632
@Dan-RAI Dan-RAI added the bug Something isn't working label Apr 19, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

2 participants