[BioC] (no subject)

John Zhang jzhang at jimmy.harvard.edu
Thu Jan 14 18:43:55 CET 2010


There is a better way of finding commonly altered regions/genes across samples 
using the CNTools and cghMCR packages. Please read the vignettes of the two 
packages in the release (2.5) or devel track. The tools do take the segment list 
of CBS as the input.


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>From: Luz G Alonso <lgarcia at cipf.es>
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>Dear J Zhang,
>I'm a PhD student.
>I was looking for a package that provides functions to identify minimum common 
>genomic regions of interests based on segmented copy number data from 
>multiple samples. I've found yours could be very useful for me. 
>Your Manual shows how to generate the segment data based on raw data using 
>DNAcopy package, and then, use these segment data (as a DNAcopy class object) 
>as the input to the cghMCR function. My problem is I've generated the segment 
>list using other method. This segment list has the same parameters than the 
>segment list you use as example (called "segData") but it is a data frame 
>object, not a DNAcopy object like "segData". 
>How could I apply cghMCR and MCR functions using my R data frame? There is 
>some method to get a DNAcopy class object from my segment list? 
>Luz G Alonso	lgarcia at cipf.es
>PhD Student
>Bioinformatics and Genomics Department
>Centro de Investigaciones Principe Felipe
>Avda. Autopista Saler 16,
>46012 Valencia, Spain
>Phone: +34 96 328 96 80
>Fax:   +34 96 328 97 01
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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