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clagiamba / moloc

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moloc analysis of GWAS summary data from case-control studies #4

Open AI-10 opened 2 years ago

AI-10 commented 2 years ago

hi, Can moloc be used for co-localization analysis of GWAS data from multiple case-control studies?

clagiamba commented 2 years ago

Hi AI-10,

Yes absolutely. One of the applications of moloc can be to colocalize genetic variants in a region (locally) across multiple GWAS datasets. You would just need to split your data into regions (usual lengths for regions range from 200kb to 1Mb).

Cheers, Claudia

AI-10 commented 2 years ago

If I perform co-localization of three GWAS obtained from binary phenotypes, how do I set it up? moloc asks for sdY,how to calculate sdY for binary phenotypes GWAS？ thanks Weiming Gong

clagiamba commented 2 years ago

Hi Weiming, If you have a case-control, sdY can be derived from s, the proportion of samples in the dataset that are cases. In moloc this is done by supplying both the N and the Ncases.

For the set-up, Must have columns SNP or CHR and POS; BETA, SE; N and MAF (to estimate sdY); if a case control: Ncases. Please see https://github.com/clagiamba/moloc/blob/master/vignettes/my-vignette.Rmd.

Please let me know if something is not clear. Thank you, Claudia

AI-10 commented 2 years ago

Many thanks, Claudia, I am using moloc in my work and it helps me a lot.

Best, Weiming