Skip to main content
Fig. 2 | Genome Biology

Fig. 2

From: Methods for copy number aberration detection from single-cell DNA-sequencing data

Fig. 2

The three approaches for segmentation. In all three panels, a scatter plot of the read count per bin with respect to the genomic position of the bin is shown. a The sliding-window approach. A window is passed across the genome, and a genomic region within a window that is significantly different in terms of read count from the rest of the genome (e.g., the window defined by the two dotted vertical lines) is declared as a segment. b The objective function-based approach. Three piecewise constant functions are shown (two in red and one in green) and represent segmentation candidates. Each piece in the function corresponds to a segment, and the value of the piece corresponds to the copy number at that segment. The function in green is the optimal one with respect to the fidelity to the data and the constraint on the number of breakpoints, whereas the two in red are either over-segmented (top) or under-segmented (bottom). c The HMM-based approach. States of the HMM correspond to the different copy numbers, and a transition between two different states indicates a change in the segment. In the read-count panel, colors of the dots represent the absolute copy number of the various genomic bins (red for 1, yellow for 2, and green for 4) as obtained by parsing the data with respect to the HMM (bottom). The actual path of the state transitions is shown in the middle and highlighted with blue arrows on the HMM as well. The arrows are numbered to indicate the order of the transitions

Back to article page