I have some question about the CopywriteR package:
1) I have observed that CopywriteR did not detect any copy number variations (CNVs) in normal samples. Is it possible to use CopywriteR for CNV detection?
2) What’s the large gap inside chromosome?(e.g. chr1,chr9) is this regions “blacklist”?
3) Is there any cut-off value for judging whether CNV exist or not?
4) Can I extract candidate genes or sites of amplification or deletion using your algorithm?