Extract an LD matrix from vcov?

[mikelove]

Is it possible to extract a text-based (covariate adjusted) LD matrix from the vcov files?

I read over https://corbinq.github.io/apex/doc/mode_store/ but didn't see this use case.

For example, something like what we would obtain from plink --file mydata --r

[corbinq]

The easiest way to do this currently is through the R script, Apex2R: https://github.com/corbinq/apex2R https://github.com/corbinq/apex2R/blob/master/example.r The R script is gene-centric; given a gene name, you can extract the covariate-adjusted LD matrix for all SNPs in the cis-region. We also had some command-line region-based vcov querying options for debugging, but they are non-functional in the current version. If there is interest, we can add back in.

…

-Corbin

On Tue, Aug 24, 2021 at 9:46 AM Mike Love ***@***.***> wrote: Is it possible to extract a text-based (covariate adjusted) LD matrix from the vcov files? I read over https://corbinq.github.io/apex/doc/mode_store/ but didn't see this use case. For example, something like what we would obtain from plink --file mydata --r — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAWQAM3BBPK6UQH442MKUQTT6PEHHANCNFSM5CXHQ7EQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[mikelove]

Thanks for the quick reply.

We'll try out the R script and see if there are any bottlenecks doing it this way.