Average odds ratio per linkage disequilibrium or haplotype block?
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4.7 years ago
Peixe ▴ 660

Hi,

I have genotypes & summary statistics for a GWAS. Through PLINK, (which uses Haploview algorithm, Gabriel S, 2002) I have generated haplotype blocks in my data. To generate larger blocks I gave the algorithm a somewhat "relaxed" threshold, so that not all SNPs inside blocks are in perfect LD.

The question is:

Is there any procedure to assign each of these blocks a sort of "average" odds ratio, in a way that at the end each block has a single value of effect size assigned, derived from a weighted average (or similar) of all the SNPs within each block?

Not sure if this is something that has been tried before...

Any help appreciated!

Thanks!

SNP linkage disequilibrium GWAS • 723 views
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