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Biometris / statgenGWAS

See https://biometris.github.io/statgenGWAS for a full description
https://biometris.github.io/statgenGWAS/
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effect of the covariate #13

Open lzhangUT opened 7 months ago

lzhangUT commented 7 months ago

Hi, Thanks for providing this package, I gave it a try, it worked pretty well for my dataset. however, I have one question regarding the covaraite. So I have a usual covariate (not snp covariate), like sex (they are coded as 0s and 1s). I used it in my GWAS model as fixed effect, it worked. but in my case, I am more interested into the effects from the covariate. I checked the output from my GWAS results, it doesnt seem to output the effect from the fixed effect. Is there a way to get the effect from covariate? Thank you.

BartJanvanRossum commented 7 months ago

I think the short answer to this would be no. At the moment there is no way of getting the effect size for the fixed effect. Including this would mean quite a big change in the current code. Unless there are multiple people that have similar requests I don't plan on investing time in this at the moment.