determination of the distribution of the PCHAT test statistic under the null hypothesis; 200 and 50 subsets and bagging subsets, respectively, for testing the association of a genetic variant with the trait; 150 individuals for the subsets; and 1000 simulations for determination of the distribution of the test statistic under the null hypothesis. The option “both” was used for the analysis, resulting in a permutation experiment to determine the null distribution of the test statistic, after which the association test is performed using the standard deviation and degrees of freedom obtained in the permutation test. PCHAT produces 11 output files. In one of them, the association result is expressed as a p-value, which was extracted for this study.
