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

[Qian Liu]

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)

Thanks,
Qian