The linear regression model is also applied when Y is a binary phenotype. Although this violates some assumptions of the F-test, comparison of the F-test p-values with p-values based on permutation of the F-statistic shows that the F-test remains accurate (see ‘Supplemental Methods—Implementation Details’). MAGMA therefore uses the asymptotic F-test p-values by default, though it also offers an option to compute permutation-based p-values using an adaptive permutation procedure. In addition, comparison with logistic regression models shows that the results of the linear model are effectively equivalent to that of the more conventional logistic regression model, but without the computational cost.
