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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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X-chromosome fine-mapping #145

Closed daxxio closed 1 year ago

daxxio commented 1 year ago

Hey, first off thank you for developing and sharing PolyFun.

I recently wanted to start a SuSiE analysis of the X-chromosome via PolyFun, but realized that it seems to not be supported.

Do you think it would be possible to do in a sex-limited sample, with e.g. also sex-limited genotype data instead of a LD reference? I was thinking to try working around it by making the X-chromosome look like an autosome, but wanted to check if this is safe.

omerwe commented 1 year ago

@daxxio good question! I believe that using an X-chromosome that looks like an autosome should be fine. Of course, you should think carefully if the model's underlying assumptions (additive effect of each minor allele on the phenotype) is appropriate and sensible in this case.