Fig. 1

Circular Binary Segmentation (CBS) - and Piecewise Constant Fit (PCF) - segmented data (amplifications). Significant copy number alterations (gains, colored in red) are illustrated in four different cohorts; breast, ovarian, endometrial, and cervical cancers, determined by two different segmentations algorithms PCF and CBS. Both methods allow the trade-off between sensitivity and specificity to be controlled by the user using the significance level for accepting a change point (α) in CBS and the penalty parameter (γ) in PCF. We selected γ = {14, 12, 14, and 16} for the PCF-segmentation and α = {0.02, 0.02, 0.02, and 0.01} for the CBS-segmentation. The statistical significance of the aberrations is displayed as FDR q-values to account for multiple-hypothesis testing (x-axis). Chromosome positions are indicated alongside the y-axis with centromere positions indicated by dotted lines. The significance threshold is allocated by a green line