Is r^2 equivalent to the squared pearson correlation?
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Entering edit mode
6.3 years ago
bbio ▴ 90

Is the r^2 between two SNPs (the measure of linkage disequilibrium between two variants) the same as the squared Pearson correlation between the two variants (encoded as 0/1/2)? In other words, to calculate the r^2 can I just take the two vectors of 0/1/2s, calculate the Pearson correlation and square the result?

Some sources seem to suggest that it is (and it would make a lot of sense to me) but I am having trouble finding a clear answer to this.

snp vcf r2 • 2.8k views
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Entering edit mode
6.3 years ago

Yes, r^2 between SNPs is a squared Pearson correlation and yes, you can compute it with the 0,1,2, coded vectors. I think this is how PLINK does it.