Figure 3.

Definitions for the evaluation of copy number detection methods. A genome is split into equally sized evaluation segments of a length shorter than the shortest CNV. Top panel: Knowing the true CNV regions (green), the evaluation segments are labeled as class 1 (CNV segment) or class −1 (non-CNV segment). Middle panel: A CNV detection method classifies each evaluation segment into CNV segments (blue, class 1) and non-CNV segments (class −1). Bottom panel: In the first line, positives (known CNV regions) are divided into true positives (TP, green) and false negatives (FN, red). In the second line, negatives (no overlap with known CNV regions) are divided into true negatives (TN, green) and false positives (FP, red). Segments partly overlapping with known or predicted CNV regions are not considered (‘na’).