Figure 2.

Illustration of the basic concept of cn.MOPS: a CNV call incorporates the detection of variation across samples (I/NI call) and the detection of variation along a chromosome (segmentation). Curves show read counts along one chromosome for five samples. I/NI calls (green) detect variation across samples (green vertical boxes). A CNV (red box) is called if consecutive segments have high I/NI calls. Blue boxes mark segments that segmentation algorithm of class (a) methods (see the ‘Introduction’ section) would combine into a CNV. First vertical bar (from the left) and first sample: the I/NI call indicates variation across samples (‘I/NI call +’). However, too few adjacent segments show high I/NI calls. Second bar and third sample: the I/NI call indicates variation across samples (‘I/NI call +’) and sufficiently many adjacent segments show high I/NI calls, which leads to a CNV call (red box). Third bar: the read counts drop consistently and would thus be detected by a segmentation algorithm of class (a) methods (blue boxes). However, the read counts of the samples do not vary, which does not lead to an I/NI call (‘I/NI call −’). A CNV is not detected, which is correct as the copy number does not vary across samples. Fourth bar and samples numbers 2 and 4: I/NI call indicates variation across samples (‘I/NI call +’). As in the first bar, too few adjacent segments show high I/NI calls. Fifth bar and second sample: a segmentation algorithm of class (a) methods would combine adjacent read counts that are consistently small (blue box) into a CNV. However, the read counts are within the variation of the constant copy number at this location. Therefore, the I/NI call does not indicate variation across samples (‘I/NI call −’).