To test for allele frequency differences between geographical regions, we used the R function snp.lhs.tests, which is part of the snpMatrix package and described in ref. 26. The SNP genotype was treated as the dependent variable (a binominal variate with two ‘trials’). Case-control status was fitted as a covariate, and region, the term to be tested, was fitted as a factor. This results in an 11-d.f. test for allele frequency differences between geographical regions.
