Rawcopy copy number analysis

Question

[moritz.feigl]

Hallo,

I used the R rawcopy package to analyze my affymetrix SNP 6.0 data. This produced the segmentation and the log ratios and allelic imbalance values. Now I'm trying to analyze those, but I can't find a suitable way. I tried the packages that are stated in the rawcopy paper for further analysis and failed to apply any of them. This was mainly because all of them have practical no useful documentation. Or at least I didn't find one. Right now I started trying to calculate the gains and losses with a simple threshold method myself, but even this is tricky because I'm not sure if I use the correct outputs from rawcopy... If anyone has experience with the rawcopy output and its further usage, I would be extremely happy to get some advice.

[sofie_carolina]

Is this problem resolved ?

[hu19930121]

Hi jgarce recently, I have run the rawcopy program on my snp6.0 data, and i don't understand the segmentation output(segments.txt). could it be the input data for GISTIC2.0, but it still missing the n.probes values for input data.
follow your sugggestion, i used copynumber package for additional segmentation (use the segments.txt as the input). finally, the segments was achieved, but the segments is so litter. could be something wrong.

Answer 1

[jgarces]

Hi Moritz,

I'll try to answer you with my (little) experience with rawcopy (and after some emails with the package's author, he's very kind):

• The correct output, I guess you mean the segmentation output, is the segments.txt file (the other ones are for generating the different plots for the QC).
• A possible method for establishing a threshold could be those contained within GISTIC2... it performs a double-step procedure: 1) it calculates a significance according the entire genome as background (this'd be the value you're searching) and 2) it searches for recurrent alterations among all your samples and gives them a score.
• And finally, after some (and not so difficult) code, you can use copynumber package for plotting (and additional segmentation if you don't like rawcopy's one.

I hope these tips help you a bit. Feel free to ask whatever you want. Bests.