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privefl / bigsnpr

R package for the analysis of massive SNP arrays.
https://privefl.github.io/bigsnpr/
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LD reference for HapMap3+ variants #411

Closed johannfaouzi closed 1 year ago

johannfaouzi commented 1 year ago

Hi,

I read the new version of the tutorial on polygenic risk scores (https://privefl.github.io/bigsnpr/articles/LDpred2.html) as well as your preprint on LDpred2-auto (https://www.biorxiv.org/content/10.1101/2022.10.10.511629v1.full.pdf). You mention the use of a new set of variants (HapMap3+). In the tutorial, you compute the LD reference on a given dataset, but it is also mentioned in the paper that:

LD matrices for HapMap3+ variants computed from the N.W. European UKBB data used in this paper are available at https://figshare.com/articles/dataset/LD_reference_for_HapMap3_/21305061

I checked the link and only the mapping file (chr, pos, a0, a1, rsid, af_UKBB, ld, block_id, pos_hg18, pos_hg38) is available if I'm not mistaken. Do you plan on providing the LD reference computed on UKBB like you did for the HapMap3 variants?

Best, Johann

johannfaouzi commented 1 year ago

Sorry, I didn't read the description. The LD reference is provided in the Google Drive folder. My bad.

privefl commented 1 year ago

No worries, you're not the first one to ask. I've added https://figshare.com/articles/dataset/LD_reference_for_HapMap3_/21305061?file=39253622, hope that helps.