My understanding of CN calling tools is that they produce a file with segments and a CN value for these segments. However, the actual number of segments as well the location of these segments vary from sample to sample (they could vary from run to run for the same sample too, I haven't tested that)
CopywriteR generates a segment.Rdata file with the following structure:
ID chrom loc.start loc.end num.mark seg.mean
There are a variable number of records generated for each sample, and the
chrom - loc.start - loc.end combinations are unique as well. Given that the above happens, is there any way I can compare the outputs generated for two different samples?