To test the hypothesis that MiXeR and LAVA-derived measures of mixed effect directions were correlated, we calculated the Pearson correlation coefficient for a) MiXeR-estimated proportion of shared ‘causal’ variants with concordant effects and b) LAVA-estimated proportion of significantly correlated genetic loci with positive correlation. These measures are comparable since both are proportions quantifying mixed genetic effects between two traits, with 0 indicative of completely discordant effects, 1 completely concordant effects, and 0.5 a balance of concordant and discordant effects. These measures differ since MiXeR estimates the effect directions of all shared ‘causal’ variants, whereas LAVA only captures significantly correlated loci.
