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getian107 / PRScsx

Cross-population polygenic prediction
MIT License
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run on chrX? #18

Closed lkachuri closed 2 years ago

lkachuri commented 2 years ago

Dear Tian,

Is it possible to get PRS-CSx to run on the X chromosome? Is it just a matter of generating the LD blocks for chrX or are there technical reasons for restricting to the autosomes?

Thanks!

getian107 commented 2 years ago

Dear Linda- We haven't incorporated X chromosomes into the PRS-CSx algorithm. Constructing PRS on X chromosomes might need special considerations (e.g. we might need to analyze males and females separately due to different dosages and the calculation of reference panels for X chromosomes may be different from autosomes which needs to be carefully validated).

lkachuri commented 2 years ago

I see, that makes sense. Perhaps something to consider for future updates :)

getian107 commented 2 years ago

Yes absolutely!