I have copy number data from cancer patients, both cancer and matched normal, that have already been segmented using DNAcopy. The problem is the segmentation function in DNAcopy had min.width set to the default of 2 producing many segments with few markers that appear more like noise than signal. My questions are:
1) Would there be any problem or concern with removing segments with low number of markers post segmentation?
2) What is the standard minimum number of markers per segment for copy number data and is there any justification or reference for this minimum number of markers?
(Ref. Manual for DNAcopy: https://www.bioconductor.org/packages/release/bioc/manuals/DNAcopy/man/DNAcopy.pdf )