Hi.
There's no direct way of doing this, but as a start you can read in
all the writeRegions()-exported segment data for all samples in a data
set as explained in
http://www.aroma-project.org/vignettes/NonPairedCBS/. That will give
you a data.frame.
>From there you should be able to manipulate the content of the
data.frame using basic R tools, e.g. subset(), rbind(), cbind() etc.
The dplyr package might be a more convenient way of doing it - it's
the ninja-tool for data.frame manipulations.
Hope this help
Henrik
PS. Feel free to share your solution here.
On Tue, Jun 20, 2017 at 10:04 AM, Emanuel Gonçalves
<emanuelvgoncal...@gmail.com> wrote:
> Dear all,
>
> I'm processing a set of ~200 SNP6 .cel files and then performing
> segmentation with CBS. But I would like to know how to extract the data
> points data-frame that is used as input to DNAcopy CBS.
>
> The code is as below:
>
> # install.packages('aroma.affymetrix', repos='http://cran.us.r-project.org')
> library("aroma.affymetrix")
>
> # Logs
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> # Reduce decimal places to minimize space
> options(digits=4)
> print('Options configured')
>
> # -- SNP6 cancer cell lines preprocessing with CRMA (v2)
> gsT <- doCRMAv2("cancer_lines", chipType="GenomeWideSNP_6,Full",
> verbose=verbose)
> print('cancer_lines CRMAv2 done.')
>
> # -- Segmentation (CBS)
> sm <- CbsModel(gsT)
> fit(sm, verbose=verbose)
> print('CbsModel done.')
>
> # -- Export segmentation
> pathname <- writeRegions(sm, verbose=verbose)
> print('Exported done.')
>
> I would like to extract the gsT as a data.frame in the format that is used
> in DNAcopy:
>
>> library(DNAcopy)
>> data(coriell)
>> head(coriell)
> Clone Chromosome Position Coriell.05296 Coriell.13330
> 1 GS1-232B23 1 0 NA 0.207470
> 2 RP11-82d16 1 468 0.008824 0.063076
> 3 RP11-62m23 1 2241 -0.000890 0.123881
> 4 RP11-60j11 1 4504 0.075875 0.154343
> 5 RP11-111O05 1 5440 0.017303 -0.043890
> 6 RP11-51b04 1 7000 -0.006770 0.094144
>
> Thank you in advance,
>
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