Hi, I have a DNAcopy object and I would like to plot just one of the samples, with one chromosome per page (so one plot per page). There are two ways I can see of doing this: 1) Subset the DNAcopy object so it only contains one sample 2) Set the plot options correctly I can not find how to do either of these. Has anyone got an idea how to overcome this. Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}

Hi Daniel -- I'm not really familiar with DNAcopy, but > library(help=DNAcopy) Information on package 'DNAcopy' [...] subset.CNA Subset a 'Copy Number Array' data object subset.DNAcopy Subset a DNAcopy data object [...] seems to point in the right direction, and (from example(plot.DNAcopy)) > #Read in two examples from Snijders et al. > > data(coriell) > > #Combine into one CNA object to prepare for analysis on Chromosomes 1-23 > > CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330), + coriell$Chromosome,coriell$Position, + data.type="logratio",sampleid=c("c05296","c13330")) Warning message: In CNA(cbind(coriell$Coriell.05296, coriell$Coriell.13330), coriell$Chromosome, : array has repeated maploc positions > > #We generally recommend smoothing single point outliers before analysis > #Make sure to check that the smoothing is proper > > smoothed.CNA.object <- smooth.CNA(CNA.object) > > #Segmentation at default parameters > > segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose=1) Analyzing: c05296 Analyzing: c13330 gets me a 'DNAcopy' object. > subset(segment.smoothed.CNA.object, 1) ID chrom loc.start loc.end num.mark seg.mean 1 c05296 1 468 240000 132 0.0212 32 c13330 1 0 40326 31 0.0834 33 c13330 1 46617 156276 51 -0.0217 34 c13330 1 156678 240000 47 0.5179 seems to get me chromosome 1, ready for plotting with > plot(subset(segment.smoothed.CNA.object, 1, 1), type="c") The 'DNAcopy' object is an 'S3' object whose struture can be interogated with > str(segment.smoothed.CNA.object) List of 3 $ data :Classes 'CNA' and 'data.frame': 2271 obs. of 4 variables: ..$ chrom :Class 'AsIs' int [1:2271] 1 1 1 1 1 1 1 1 1 1 ... ..$ maploc: int [1:2271] 0 468 2241 4504 5440 7000 9046 10000 12618 13000 ... ..$ c05296: num [1:2271] NA 0.00882 -0.00089 0.07587 0.01730 ... ..$ c13330: num [1:2271] 0.2075 0.0631 0.1239 0.1543 -0.0439 ... ..- attr(*, "data.type")= chr "logratio" $ output:'data.frame': 77 obs. of 6 variables: ..$ ID : chr [1:77] "c05296" "c05296" "c05296" "c05296" ... ..$ chrom : int [1:77] 1 2 3 4 4 4 5 6 7 8 ... ..$ loc.start: int [1:77] 468 0 0 0 172856 179200 0 0 0 0 ... ..$ loc.end : int [1:77] 240000 245000 218000 171809 179118 184000 198500 188000 161500 147000 ... ..$ num.mark : num [1:77] 132 64 86 143 9 13 108 85 172 151 ... ..$ seg.mean : num [1:77] 0.0212 0.0095 0.0025 -0.0085 0.1752 ... $ call : language segment(x = smoothed.CNA.object, verbose = 1) - attr(*, "class")= chr "DNAcopy" This is a simple list, and the 'data' and 'output' element looks like readily understandable data frames containing information that we might like to extract and use for our own, fancier, lattice plots. Martin Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> writes: > Hi, > > I have a DNAcopy object and I would like to plot just one of the > samples, with one chromosome per page (so one plot per page). There are > two ways I can see of doing this: > 1) Subset the DNAcopy object so it only contains one sample > 2) Set the plot options correctly > > I can not find how to do either of these. Has anyone got an idea how to > overcome this. > > Thanks > -- > ************************************************************** > Daniel Brewer, Ph.D. > Institute of Cancer Research > Email: daniel.brewer at icr.ac.uk > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the addre...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org