Re: [aroma.affymetrix] CBS input dataframe

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

Re: [aroma.affymetrix] CBS input dataframe

Ah, my bad - you're correct. On Tue, Jun 20, 2017 at 4:40 PM, Emanuel Gonçalves wrote: > 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 >

Re: [aroma.affymetrix] CBS input dataframe

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

Re: [aroma.affymetrix] CBS input dataframe

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

[aroma.affymetrix] CBS input dataframe

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',