I came across a quantitative measure of Hardy-Weinberg equilibrium (HWE). It is due to Olson and Foley and it is very simple:
theta = H^2 / (4PQ) = (2pq)^2 / (4p^2q^2),
where H is the frequency (probability) of heterozygotes (say A/B), P is the frequency of "first" homozygotes (say A/A), Q likewise for other homozygotes (say B/B), and p and q are the allele frequencies for alleles A and B, respectively. Under HWE theta equals 1, since P = p^2, H = 2pq, and Q = q^2. Too many heterzygotes will rise the theta above 1, while theta bellow one would correspond to too few heterzygotes. I like this measure. Up to now I have done quite some tests of HWE using the Chi-square test or the MCMC method (see above link for the details), but I never really checked what is the reason for deviation from HWE. A measure by Olson and Foley can shed some more light.
Olson JM, Foley M (1996) Testing for homogeneity of Hardy-Weinberg disequilibrium using data sampled from several populations. Biometrics 52: 971–979.
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