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n-mounier / MRlap

R package to perform two-sample Mendelian Randomisation (MR) analyses using (potentially) overlapping samples
GNU General Public License v2.0
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TwoSampleMR::clump_data requires an active internet connection #2

Open sjfandrews opened 3 years ago

sjfandrews commented 3 years ago

Hi,

In applying MRlap I ran into the issue of LD clumping using TwoSampleMR::clump_data requiring an active internet connection. When no internet connection is available this will cause MRlap to fail. This can be an issue when submitting to jobs compute cluster.

A potential solution to this is using ieugwasr::ld_clump (which clump_data calls) with the option of specifying a local plink binary and LD reference to perform clumping locally.

Thanks!

lcpilling commented 11 months ago

This feature has now been implemented with PR #10

You can use a local installation of Plink for LD clumping with a custom reference panel (using MR_plink and MR_bfile options)