I think what I'm looking for is: extractRawCopyNumbers(cbsmodel, array=1, chromosome=2)
Problem is I have ~200 and the function seems to be taking quite sometime to get me the results (is this because I don't have all the cbs computed yet?), is there a way to export the whole data-set raw copy numbers? Thank you, On Tuesday, June 20, 2017 at 10:33:36 PM UTC+1, Emanuel Gonçalves wrote: > > 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 >> > 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. >> > 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.
