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, > > > > -- > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest > > version of the package, 2) to report the output of sessionInfo() and > > traceback(), and 3) to post a complete code example. > > > > > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to aroma-af...@googlegroups.com > <javascript:> > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to aroma-affymetr...@googlegroups.com <javascript:>. > > For more options, visit https://groups.google.com/d/optout. > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.