The effect of changing the penalty γ in PCF. The plot in the upper left corner shows the copy number data for a selected chromosome (in this case, chromosome 17), while the lower right plot shows the number of segments found by PCF as a function of γ. The remaining plots show the segmentation curves for ten different values of γ. The plot was created with the function plotGamma in copynumber.
Nilsen et al. BMC Genomics 2012 13:591 doi:10.1186/1471-2164-13-591