Turning now to a Bayesian approach we assume Dir(1,1,1) priors under the alternative and compare results based on two priors under the null, namely Dir(1,1) and the triangular distribution, equation (8). In terms of computation time, the Bayes factor calculations took approximately half the time of the exact p-values (which were calculated using the hwexact function in R). In Figure 4d, we plot –log10 Bayes factors (under the conjugate prior) versus –log10 p-values (from the exact test), and we see a very close correspondence, particularly for the SNPs that deviate from HWE.
