[BioC] Circular binary segmentation for allele-specific CN data

[Christine Ho]

Good afternoon!

I hope this question is not redundant - I've tried searching the  
mailing list archives and doing a Google search.

I've just finished using aroma.affymetrix() to produce allele-specific  
copy number estimates. So, right now, I've got the allele frequency  
data, i.e. what the vignettes call "fracB" data. I would like to run  
circular binary segmentation on this to find breakpoints (so I can  
identify regions of LOH), but it seems that all of the related  
packages on Bioconductor just segment aCGH data.

So, I was wondering: are the segmentation algorithms in these packages  
(for ex., snapCGH) able to handle any dataset, or are they specific to  
aCGH data? If they are specific to aCGH data, would anyone happen to  
know where I can obtain code (or better yet, a package) for running  
CBS on any data set?

Thank you for your time! I really appreciate it.

Best,
Christine Ho
Graduate student in Statistics at UC Berkeley
E-mail: cho at stat.berkeley.edu