Fig. 2

Summary and examples of performance metrics. a Schematic overview of classes of frequently used performance metrics, including examples (boxes outlined in gray). b Examples of popular visualizations of quantitative performance metrics for classification methods, using reference datasets with a ground truth. ROC curves (left). TPR versus FDR curves (center); circles represent observed TPR and FDR at typical FDR thresholds of 1, 5, and 10%, with filled circles indicating observed FDR lower than or equal to the imposed threshold. PR curves (right). Visualizations in b were generated using iCOBRA R/Bioconductor package [56]. FDR false discovery rate, FPR false positive rate, PR precision–recall, ROC receiver operating characteristic, TPR true positive rate