[BioC] CGH DNAcopy plot multiple samples on one plot

[Gavin Kelly]

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