Calculating linkage disequilibrium

Linkage disequilibrium (D) measures the deviation from linkage equilibrium. It can be calculated as follows:

In a two loci, two allele model there are four possible haplotypes.

Let each haplotype's frequency be:

PA1B1, PA1B2, PA2B1, PA2B2

The linkage disequilibrium can be defined as

D = PA1B1 * PA2B2 - PA1B2 * PA2B1

D measures the deviation from linkage equilibrium. If D > 0 there are an excess of A1B1 (and A2B2) haplotypes: A1 is more often found with B1 (and less often with B2) than would be expected if they combined at random.