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qlu-lab / PUMAS

Fine-tuning polygenic risk score models using GWAS summary statistics
MIT License
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binary traits #10

Closed lgarvert closed 1 year ago

lgarvert commented 1 year ago

Hi, I read in your paper that PUMAS is also applicable to binary traits. Does this require any special formatting/recoding of my input file or does it automatically recognize ORs in the BETA column?

Thanks! Linda

zijie02 commented 1 year ago

Hi Linda,

Thank you for posting this comment. Yes PUMAS can be applied to binary traits. We haven't provided the script for GWAS QC/reformatting so far. We are working on that and the added script will first clean user input GWAS and then output reformatted summary statistics. Binary GWAS summary statistics obtained from logistic regression will be transformed to observed scale. We'll make it available very soon.

Best, Zijie

qlu-lab commented 1 year ago

Hi Linda,

Apologies for the delayed update. We have uploaded the script and tutorial for cleaning GWAS summary statistics. The script will output summary statistics formatted for PUMAS/PUMACUBS. Please feel free to try it out and let us know if you encounter any issues.

Zijie