Figure 2

Naïve combination is not better than individual methods for PMD_HUMAN data. This figure shows accuracy-coverage curves for the PMD_HUMAN data. The x-axes indicate coverage (also referred to as 'recall'; Eqn. 1.2), i.e. the percentage of observed neutral (a) and of observed effect (b) variants that are correctly predicted at the given threshold. The y-axes indicate accuracy (also referred to as 'precision'; Eqn. 1.2), i.e. the percentage of neutral (a) and effect (b) variants among all variants predicted in either class at the given threshold. Arrows mark the performance at the default thresholds for our new method SNAP2 (dark blue), for SIFT (green), and for PolyPhen-2 (orange). A brown triangle/arrow marks the performance of a (non-optimized) method that combines PolyPhen-2 and SIFT. This combination did not perform better than SNAP2 alone (brown triangle vs. blue SNAP2 curves).