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

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Fri Aug 20 19:15:29 CEST 2010

CBS just does a segmentation on any kind of vector data using a
conceptually simple algorithm, there is no reason why you couldn't run
it on whatever data you have.

Of course, your data might be behaving a bit different wrt. scale,
outliers etc. that can all have effects on the quality of the
segmentation.  Often the devils are in the details.

If you look at the structure of the DNA objects in DNAcopy it ought to
be simple to see how you can put whatever you have in there.  It is
essentially a vector of positions and a matrix of data.

Having said all of this, you should ask on the aroma.affymetrix email
list, I am sure that there are people with experience with running CBS
on alle-specific copy number.


On Thu, Aug 19, 2010 at 3:54 PM, Christine Ho <cho at stat.berkeley.edu> wrote:
> 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
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