observed P-values in the 244 common CNVRs with those quantiles of approximate exact P-values based on 1000 permutations in the case–control sample and the family-based sample, respectively. Note that here, deviations from the diagonal line for the case–control sample result from the limited number of permutations performed. CNVR-wise approximate exact (called CNVR-adjusted) P-values were calculated analogously by taking into account that several CNV markers have been tested for each CNVR. Thus here, for each permutation and each CNVR, the maximum over all CNV markers test statistics was compared with the maximum of the observed test statistic. In order to achieve one-sided exact P-values, we additionally stored and compared the direction of the effect.
