Hi Henrik,
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.
>
But that would get me the segmentation regions, right? What I want is to
export the input of CBS.
> # -- SNP6 cancer cell lines preprocessing with CRMA (v2)
> > gsT <- doCRMAv2("cancer_lines", chipType="GenomeWideSNP_6,Full",
> > verbose=verbose)
> > print('cancer_lines CRMAv2 done.')
>
In other words, is there a writeRegions function for "gsT" to export it as
a table with the probe, chromosome, position and the ratios per sample.
Thank you for your time,
>
> > # -- 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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