The function takes as an input a set of intervals with integer-valued boundary positions. It then finds interval regions where the event count is above each of two thresholds, upper and lower, and returns those interval regions with the count above the lower threshold that contain interval regions with the count above the upper threshold.
A mask is applied to amplified or deleted segments as tabulated in segtable. A decision whether to mask a segment is taken based on what portion of the segment is covered by the mask. A position is chosen at random within a segment to be masked, the flanking segments are extended to that position and the segment to be masked is indicated as such in the value returned.
Description: The package evaluates DNA copy number data, using both their intitial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm.
providing 
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