Figure 2.

Box-Plots of Empirical Type 1 Errors and Statistical Powers of Various PPI-Based Association Tests

(A–C) Empirical type 1 error (A); power under the alternative hypothesis A (B); and power under the alternative hypothesis of B (C), for the various PPI-based association tests. Detailed descriptions of the two alternative hypotheses are available in the Material and Methods section. Note that Fisher’s and Stouffer’s methods were excluded in the power comparison because of inflated type 1 error rates. Fisher: the Fisher’s combination test combining two gene-based p values calculated by GATES; Stouffer: Stouffer’s Z transform method combining two gene-based p values calculated by GATES. The following abbreviations are used: W.HYST, HYST with arbitrary weights (1:5 for SLC3A1:CAMKMT); ScaleChi, scaled chi-square test; LKM: the Logistic Kernel Machine Test.