Raw copy numbers for sample NA12763 in a chromosome 12 region. (a) Raw copy numbers R
. (b) The smooth signal R
*, obtained by applying the low pass filter to R
. The green colored markers indicate a 'gain' class value assignment, whereas the red markers indicate 'normal' class assignment by the edge detection algorithm. Note that there are two candidate gain regions in the figure. (c) Our objective function optimization using simulated annealing makes the final assignments to the markers and it merges the two candidate regions in (b) into one gain region.