LD matrix calculations

[npanousis]

Hello,
Thank you for providing the code for these plots. This is not a bug report but more a question.
How do you calculate the correlation matrix with LDlink since the API allows only 1000 variants? Any help would be appreciated.

Thanks a lot,
Nikos

[jrs95]

Hi Nikos,

Yes, this can be a problem for larger regions.

Perhaps the IEU GWAS R package ld_matrix function could do the trick. Although, if you are wanting to plot a lot of regional plots you might be better off downloading the 1000G VCFs and writing a small script to compute the LD.

Best wishes,

James