LD proxies for TwoSampleMR

Downstream analysis with genomic data
1

Hi everyone!

Does anyone have a nice guide for adding in LD proxies for missing SNPs in outcome GWAS for use in two sample mr?

Thanks so much!

2

For anyone’s future reference here are basic options:
1.) Identify missing SNPs you want LD proxies for (I did this in two sample MR, by extracting significant exposure snps from the outcome gwas and set.difference between the two.)

2.) With your sum stats in the gwasvcf package, your list of proxies you want, and a bfile of local LD scores, you can simply use the function get_ld_proxies().

3.) Otherwise use LD link to manuall look up and modify your LD proxies in your sum stats one by one.