Hi,

I have used the segmented data and obtained copy number (CN) states: loss, gain and balanced for genomic regions in each sample. I want to summarize these CN states for each chromosomal arm for a subset of samples (say, groups A and B). Considering non-overlapping regions across samples, is it good to average segmented values for the regions within a chromosomal arm and then use a threshold to derive a CN state for the arm? If not, are there any better ways to do this?

Many thanks,
Ezhil