Question

CGH DNAcopy plot multiple samples on one plot

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Daniel Brewer ★ 1.9k

@daniel-brewer-1791

Last seen 9.6 years ago

Hi, Is there anyway to plot the results of DNAcopy for all or some samples on one plot? Just the segments not the underlying data points. This is to allow visual comparison of samples. Many thanks Dan -- ************************************************************** 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 a...{{dropped:2}}

Cancer DNAcopy Cancer DNAcopy • 1.3k views

ADD COMMENT • link updated 16.4 years ago by Gavin Kelly ▴ 50 • written 16.4 years ago by Daniel Brewer ★ 1.9k

score 0 · Answer 1 · 2007-11-13

Dear Dan, This migt be (only a little) bit more complicated than you wanted, but the structure of the objects returned by DNAcopy is straightforward enough that you can take that, "stretch" the segments, and just plot them. In case it helps, we do that in some of the plots of our web tool http://adacgh2.bioinfo.cnio.es, that uses the ADaCGH package from CRAN (http://cran.r-project.org/src/contrib/Descriptions/ADaCGH.html). Best, R. On Tuesday 13 November 2007 12:10, Daniel Brewer wrote: > Hi, > > Is there anyway to plot the results of DNAcopy for all or some samples > on one plot? Just the segments not the underlying data points. This is > to allow visual comparison of samples. > > Many thanks > > Dan -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}}

score 0 · Answer 2 · 2007-11-13

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Gavin Kelly ▴ 50

@gavin-kelly-1449

Last seen 9.6 years ago

Daniel Brewer wrote: > Hi, Is there anyway to plot the results of DNAcopy > for all or some samples on one plot? Just the segments > not the underlying data points. This is to allow visual > comparison of samples. Many thanks Dan In the snapCGH you can have their version of DNAcopy (runDNAcopy), and you can overplot as many segmented genomes as you want with the plotSegmentedGenome command. It's a bit of a roundabout way, you may have to make multiple copies of your segmentations, and then permute the array indices in one copy to make sure the arrays you want to plot are all at the same index, but it should do it. What I do nowadays, though, is export the values out as a text file, and then load them into affymetrix' Integrated Genome Browser, where you can load and superimpose as many tracks as you want. I'll try to get around to making available my code for doing this. Hope this helps - Gavin

ADD COMMENT • link 16.4 years ago Gavin Kelly ▴ 50

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On Nov 13, 2007 7:56 AM, Gavin Kelly <gavin.kelly at="" cancer.org.uk=""> wrote: > Daniel Brewer wrote: > > Hi, Is there anyway to plot the results of DNAcopy > > for all or some samples on one plot? Just the segments > > not the underlying data points. This is to allow visual > > comparison of samples. Many thanks Dan > > In the snapCGH you can have their version of DNAcopy (runDNAcopy), and > you can overplot as many segmented genomes as you want with the > plotSegmentedGenome command. It's a bit of a roundabout way, you may > have to make multiple copies of your segmentations, and then permute the > array indices in one copy to make sure the arrays you want to plot are > all at the same index, but it should do it. > > What I do nowadays, though, is export the values out as a text file, and > then load them into affymetrix' Integrated Genome Browser, where you can > load and superimpose as many tracks as you want. I'll try to get around > to making available my code for doing this. Along the same lines, one can make pretty nice plots using the UCSC genome browser, also. One can use the "data" to make a wiggle track, or one can simply color-code the regions of gain/loss and make bed tracks. The latter option keeps the filesize down and allows one to quickly view the results of segmentation for dozens of samples. The file formats for the UCSC genome broswer pretty simple. Descriptions are available here: http://genome.ucsc.edu/goldenPath/help/customTrack.html Sean

ADD REPLY • link 16.4 years ago Sean Davis 21k