max and sum gene scores, respectively. P-values can be estimated by phenotype label permutation, but this method is both computationally intensive and requires access to genotype data of the actual study, which are rarely shared[15]. Thus, one often has access only to association summary statistics and not the individual genotypes. In this case, one method is to regress out confounding factors[3]. This approach is employed in the popular MAGENTA tool, but provides only a partial solution as substantial residual confounding still remains[3].
