Figure 4.

Power Comparison of SPAGE, CML, and EB Tests

Empirical powers were estimated based on ${10}^5$ simulated variants with ${\beta }_G=0$ and ${\beta }_{G\times E}\ne 0$. From top to bottom, the plots show empirical powers when testing variants with MAFs of 0.01, 0.05, and 0.3. From left to right, the plots consider case-control ratios of 25,000:25,000 (balanced), 5,000:45,000 (moderately unbalanced), and 500:49,500 (unbalanced). p values of CML (constrained maximum likelihood) and EB (empirical Bayes) were calculated via an R package CGEN. Round points are for powers at $\alpha =5\times {10}^{-5}$ and triangle points are for powers at $\alpha =5\times {10}^{-8}$.