Question: Analysing WGS data with CNAnorm: Extracting Copy Number from CNAnorm data
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gravatar for kuanyang.chew
2.6 years ago by
kuanyang.chew0 wrote:

Hi,

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

cnanorm next-gen • 771 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by kuanyang.chew0
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