 Allelic correlation

For two segregating biallelic loci, encode the allele on a random population haplotype by indicator variables $X,Y$. Their covariance is the linkage disequilibrium coefficient $D$. The squared correlation is $r^2=D^2/[p_A(1-p_A)p_B(1-p_B)]$, between zero and one. It measures how well one marker predicts the other and is undefined if either marker is monomorphic.

// Target: biology.bigb