I am very interested in using your CopywriteR technique to analyze gains and losses from exome data. I went through the entire pipeline and have a very messy output.
It does not look nearly as clean as the examples in the copywriter paper. Am I supposed to interpret the green line at the top and red line at the bottom as gains and losses, or am I only supposed to interpret the red lines in the middle of the image as indicating gains and losses. Does this look reasonable as output or is there a way to improve it?
My plot does not look nearly as clean as what you show in your publication:
Any suggestions? Thanks so much for your help.