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MRCIEU / TwoSampleMR

R package for performing 2-sample MR using MR-Base database
https://mrcieu.github.io/TwoSampleMR
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Using local exposures in Multivariable MR #109

Open michelle-bell opened 5 years ago

michelle-bell commented 5 years ago

Hello,

I want to run a Multivariable MR (MVMR) using local GWAS summary stats for my exposures. What is the best way to read in and prepare the exposures?
I don't think I can use the mv_extract_exposures function which uses the MR-Base GWAS data to find the unique SNPs, proxies, and harmonize between exposures to get your 'final' exposure file. Is there any function that does this for local files?

Thank you, Michelle

Suus0509 commented 4 years ago

Hi Michelle,

Did you, in the mean time, figure out how to use local GWAS summary stats within MVMR? I am trying this as well, but I did not succeed yet. I look forward to hearing from you.

Thank you, Suzanne

michelle-bell commented 4 years ago

Hi Suzanne,

I did not find an integrated way to do it by just uploading my own summary statistics. I manually created the final files it uses to perform the final MVMR analysis/function. So I manually found the unique SNPs in the exposures, and pulled the summary statistics out for both. Then, found all those unique SNPs in the outcome. I had to be resourceful to settle LD and proxy SNPs. I am not sure if this is the most appropriate way, but it's all I could figure out how to do it! I found out how to create the files by running MVMR with phenotypes in the database and using them templates.