Linkage Disequilibrium can be assessed by D (better D') and r. However, to do so, you need to phase your markers (e.g. SNP), which is painful if you have a lot of them. Pearson correlation on SNP values, coded as -1/0/+1 or 0/1/2, seems to work well, also without requiring phasing. I just wonder what is the relationship between Pearson r and LD D' or r.
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