[BioC] cghMCR package - Jianhua Zhang

Luz G Alonso lgarcia at cipf.es
Tue Jan 12 17:20:38 CET 2010

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

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