I have run a Tumor-Normal sample through CNAnorm, and I have received the output. I used the function
> exportTable(CN, file = "CNAnorm_table.tab", show = 'center')
After doing that, I get a huge file with data like this:
Chr Pos Ratio Ratio.n Ratio.s.n SegMean SegMean.n chr22 22863735 NA NA NA 1.856518897 1.022403445 chr22 22863838 NA NA NA 1.856518897 1.022403445 chr22 22863941 1.692009846 0.931806672 1.10115332 1.856518897 1.022403445 chr22 22864044 NA NA NA 1.856518897 1.022403445 chr22 22864147 NA NA NA 1.856518897 1.022403445 chr22 22864250 NA NA NA 1.856518897 1.022403445 chr22 22864353 NA NA NA 1.856518897 1.022403445
One thing I noticed is that the "pos" have the same difference (103). The problem is that I don't get a copy number for a region larger than 103 bp. How do I solve this problem and get copy numbers for large regions, or how do I interpret this data? Thanks!
P.S. I have very little coding experience
Edit: I am using windows