Hi Henrik,
Thank you very much for your response. However, I tried the following
codes to set the minimal number of marker to 5, but the results I got
still contain segments with only 2 markers ...
cbs = CbsModel(ds);
cbs$.calculateRatios = FALSE;
ce = ChromosomeExplorer(cbs);
process(ce,chromosomes=c(1:23),min.width=5);
I am not clear where I should put "min.width=5"? If I do
"process(cbs,min.width=5)" first, how can I send the results to be
displayed by chromosome explorer?
Thanks again for your help. I look forward to hearing from you soon.
Best,
Kai
On Sep 27, 9:47 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
> Hi.
>
> On Mon, Sep 27, 2010 at 4:51 PM, Kai <wangz...@gmail.com> wrote:
> > Hi Henrik,
>
> > I was wondering whether there is a way I can fine tune the behavior of
> > CbsModel. Sometimes the default algorithm produces too many small
> > fragments right next to each other without much separation in mean
> > copy numbers. Is there a way to control how "smooth" the segmentation
> > results are?
>
> Any additional arguments (in "...") that you pass to process(cbs, ...)
> will be passed down to the DNAcopy::segment(), which is the function
> doing the actual segmentation. For more details on how fine tuning
> the CBS algorithm, see help("segment", package="DNAcopy"). You may
> also want to contact the authors of that method/package.
>
> /Henrik
>
>
>
> > Thanks a lot!
>
> > Best,
> > Kai
>
> > --
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>
--
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