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culling by linkage #6
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Any ideas on implementation? I haven't thought about it much as linkage pruning was a lower priority feature for me, but locus substitution (ie finding good substitutes for PRS loci that are not well-genotyped, rather than just totally giving up and imputing) would be a killer feature, and I think could use the same backend. |
I was thinking that we could calculate R2 from the observed genotypes, given a large enough cohort. Then choose, for example the single variant from a block with highest allele frequency. |
Ah yep that would work for LD pruning, though not for locus substitution. I've been thinking about adding support for something like a precomputed r2 file (https://www.cog-genomics.org/plink/1.9/ld#r) which is a good fit for the substitution problem, but would that address the linkage pruning issue for you? I think I'm not really understanding the use case for linkage pruning, so let me know if I'm barking up the wrong tree here. |
I don't have a lot of experience in this area, but I guess I'm thinking of something like this: https://www.prsice.info/step_by_step/#clumping |
Ah I see, yes for a GPRS (ie all loci w/o LD pruning in the discovery phase, coefficients from simple per-SNP tests) that would be useful to ensure that densely sampled LD blocks don't dominate the score. Something to add for genome-wide for sure, thanks. |
select only 1 site from each linkage region for the PRS summation.
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