Tuning segment() in DNAcopy package to get more segments on each chromosome
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Qian Liu ▴ 110
@qian-liu-4216
Last seen 6.8 years ago
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
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@sean-davis-490
Last seen 16 days ago
United States
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
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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 >
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