Chunk #38 — Statistical Methodology for the Analysis of Association Trajectories — Identification of significant SNPs — Significant SNPs identified by concentration of effect sizes
Permutation tests were carried out to test the null hypothesis that the distribution of the averaged absolute value of effect size values was not SNP-specific, that is, that a random distribution of the observed effect sizes among SNPs could account for the observed variability of effect sizes among SNP. To characterize the null hypothesis, the absolute values of the effect sizes from different SNPs were used when the averaging over the electrodes to create values for “pseudo”-SNPs in a manner similar to the averaging over the actual SNPs described in the previous paragraph. Since the data contains 21 SNPs, 21 pseudo-SNPs were created for each permutation calculation. For each pseudo-SNP, the average of the effect sizes over the 9 electrodes is not from a single SNP but from 9 different SNPs, no combination of which is repeated among the 21 pseudo-SNPs. That is, 9 distinct permutations of the effect sizes of the 21 SNPs are produced, one for each electrode, resulting in a matrix of 9 × 21 values for each sex-modality-age combination. Then the effect sizes are averaged across
