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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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MAF for cases and controls #127

Closed RaviBot closed 1 year ago

RaviBot commented 1 year ago

Hello!

First off thank you for this amazing package/pipeline!

I had a question regarding my summary statistics. I have a column for MAF for cases and MAF for controls, but munge does not have a way to account for this as far as I am aware of. This is the F_A and F_U in this link. Can someone please help with the best to account for this moving forward? I am not sure if a new column should be created, or if munge can take care of this somehow.

Thanks in advance!

Ravi

omerwe commented 1 year ago

Hi @RaviBot, unfortunately the code doesn't support this. You can compute a combined MAF by taking the weighted average (weighting by the proportion of cases and controls in your sample). Hope this helps, please let me know if not!