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corbinq / apex

Toolkit for QTL mapping and meta-analysis.
https://corbinq.github.io/apex/
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Extract an LD matrix from vcov? #9

Closed mikelove closed 2 years ago

mikelove commented 3 years ago

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 commented 3 years ago

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

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mikelove commented 3 years ago

Thanks for the quick reply.

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