segment default parameters

[laugon10]

Hello,
I am working with DNAcopy, trying to really understand the parameters in order to choose the best ones for my samples.
I have tried DNAcopy without specifying anything -> default parameters I guess the ones specified in the manual

segments.CNA.object <- segment(smoothed.CNA.object,verbose=1)

In the manual
segment(x, weights = NULL, alpha = 0.01, nperm = 10000, p.method = c("hybrid", "perm"), min.width=2, kmax=25, nmin=200, eta=0.05, sbdry=NULL, trim = 0.025, undo.splits = c("none", "prune", "sdundo"), undo.prune=0.05, undo.SD=3, verbose=1)

But when I run the same sample with the specified defaults I obtained a different result

segments.CNA.object <- segment(smoothed.CNA.object, weights = NULL, alpha = 0.01, nperm = 10000, p.method = "hybrid", min.width=2, kmax=25, nmin=200, eta=0.05, sbdry=NULL, trim = 0.025, undo.splits = "none", undo.prune=0.05, undo.SD=3, verbose=1)

Are really these the default parameters? Maybe I am misunderstanding the documentation.

Thank you very much in advance. I really want to understand this.

Laura G.