Dear Sean, Thanks for your reply. "window" is from the literature Biostatistics. 2004 Oct;5(4):557-72. Circular binary segmentation for the analysis of array-based DNA copy number data. Olshen AB, Venkatraman ES, Lucito R, Wigler M. On page 560 "the permutation approach is computationally intensive. ...Our solution is to divide the data into K overlapping windows...." The reason I ask is that I dont understand how "kmax" and "nmin" in segment() are used in calculating segments, and where do you set the window size in the segment(). I really appreciate it if someone explain this to me. Thanks, Qian On Mon, Nov 14, 2011 at 3:20 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > 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. > > Sean >