Comments (1)
Hi ,
Yes! All of the above mentioned points are valid. Proper method would be to look at the segments rather than just the change points. I have tried different methods, for instance CBS segmentation and cumulative segmentation (which are intended for copy number data), but they are sensitive to low mutation burden and often results in false positives in this case.
As you have mentioned, user would be able infer segments from adjacent change points (with help of generated plot), however I too have observed instances where changepoint would simply return start locus or end locus. But, of all the methods I have tried on available datasets, this method seem to give reasonable result. I am also restricted in new datasets to verify results.
I'm currently working on an improvised method as described in original nature article by Alexandrov et al 2013, it should be up soon. Meanwhile I would really appreciate if you have any suggestion on the issue.
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