We tested for association of each factor with each SNP by linear regression of the factor against SNP genotype. For imputed SNPs and missing genotypes we used the posterior mean genotype [47]. For each SNP and factor we performed both frequentist and Bayesian tests of association: we obtained P-values using SNPTest [48] with the parameters: [-frequentist 1 -method expected -use_raw_phenotypes] and Bayes Factors (BF) using BIMBAM [47], [49] using the default parameters that average over four different prior probabilities on effect size.
