Admixed Association Tests Simulation

We calculate the ATT and Tractor association tests on simulated data using scripts that can be found on https://github.com/rachelmester/AdmixedAssociation. ATT is a 1 degree of freedom association test that uses the model $y=\beta g+e_{\alpha }^T\alpha +ϵ$ to test for β = 0 against a null hypothesis that includes global ancestry (α). Tractor is a two degree of freedom association test that uses the model $y={\beta }_1{g}_1+{\beta }_2{g}_2+e_{l}l+e_{\alpha }^T\alpha +ϵ$ to test for β₁ = 0 and β₂ = 0 against a null hypothesis that includes local ancestry (l) and global ancestry (α). They can both be adapted to be used on case-control phenotypes or to adjust for additional covariates such as age and sex. For our simulations, we used global ancestry proportions as our measure of global ancestry (α) and did not need to adjust for any additional covariates such as age and sex as we did not model those factors in our simulations. For power calculations, we use a standard significance threshold of p-value < 5 × 10⁻⁸.