[BioC] running time of snapCGH processCGH and runDNAcopy

[Henrik Bengtsson]

On 10/5/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> jhs1jjm at leeds.ac.uk wrote:
> > Hi Caimiao,
> >
> > For me, the DNAcopy segmentation function ran quicker in the actually
> > DNAcopy package than it did in the snapCGH package, not sure why but I
> > do know they made some speed improvements in the CBS algorithm that may
> > not have been implemented in snapCGH. It may be worth investigating
> > using the actual DNAcopy package, especially if snapCGH is crashing on
> > you. If anyone feels this is wrong feel to correct me, just thought I
> > should contribute as I've made heavy use of this mailing list myself!
>
> Hi, John.
>
> Just to clarify, snapCGH uses the DNAcopy package.  They are not
> different implementations.

I haven't looked at the snapCGH code, but in case it is truly slowing
things down, keep an eye on the memory overhead of your R process.  If
you're running low of memory and your OS start swapping you'll
experience a 10-1000x slowdown.  It might be that snapCGH is creating
extra/unnecessary copies.

My $.02

/Henrik

>
> Sean
>
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