I think I have a good grasp why we can use maxT permutations to adjust for multiple comparisons. However, what I do not quite understand is, how the maxT permutation helps us deal with the fact that many of our tests are not independent. The PLINK1.9 documentation it says:
Because the permutation schemes preserve the correlational structure between SNPs, this provides a less stringent correction for multiple testing in comparison to the Bonferroni, which assumes all tests are independent.
Does this mean, that during each permutation, the labels (i.e. the phenotype) only get shuffled once and then the test is performed for all SNPs and all individuals using the shuffled phenotype? Or is the phenotype shuffled for each permutation and each SNP?
If I understand everything correctly, the first statement should be correct.
I would be very grateful if somebody could tell me if this is the case, and if not, what I understood wrong!
Cheers!
