[BioC] Tuning segment() in DNAcopy package to get more segments on each chromosome

Sean Davis sdavis2 at mail.nih.gov
Mon Nov 14 21:20:06 CET 2011

On Mon, Nov 14, 2011 at 3:13 PM, Qian Liu <littleduck24 at gmail.com> wrote:
> Dear all,
> I am trying to tune segment() in DNAcopy package to generate more
> segments. Currently I have few segments in each chromosome (min 3
> segments max-7).
> I want to have a least 20 segments in each chromosome. min 5 markers
> in each segment. also the number of markers in moving window =1000.
> My 1st question is how the parameter kmax and nmin work in the cbs
> algorithm? I read the literature, but I couldn't figure it out.
> My 2nd question is in the segment function min.width=5 for min 5
> markers in each segment. So how to set the window size = 1000?
> kmax is the maximum width of smaller segment for permutation in the
> hybrid method.
> nmin is the minimum length of data for which the approximation of
> maximum statistic is used under the hybrid method. should be larger
> than 4*kmax
> segment(x, alpha = 0.01, nperm = 10000, p.method =
>                    "hybrid", min.width=5, kmax=25, nmin=200,
>                    undo.splits =  "prune",undo.prune=0.05,
>                    verbose=1)

Hi, Qian.

Try making alpha larger (0.05 or 0.1).  Leave undo.splits="none".  If
I recall, both of those will lead to more breaks.  You should be
evaluating the results by eye, though, to be sure that more breaks is
actually justified by the data.  I am not used to thinking along the
lines of "I want to see XXX number of breaks per chromosome".

I am not sure what you mean by "window", so I can't help you there.


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