To increase the generalizability of these findings, two variations on the CD analyses were performed for MAGMA-main, MAGMA-mean and MAGMA-top. First, the analyses were repeated with 10 principal components computed from the whole data set as covariates to correct for possible stratification. The results are shown in Table 2 and S10 Fig. There is shown to be only very limited stratification, and although the power does decrease somewhat MAGMA-main’s power advantage is maintained. The analyses were also repeated with the gene annotation extended to include a 10 kilobase window around each gene, with the comparison in S11 Fig showing a considerable impact on the results. However, although this suggests that the choice of window can strongly affect the results of a gene analysis Table 2 shows that the relative power stays the same, with MAGMA-main again maintaining its superior power.
