Hello,
I remember reading a while ago that you can pass in additional parameters to
CbsModel, and they will get passed onto DNAcopy functions. However, it doesn't
seem to be working for me. I don't want any segments less than 5 probes wide.
However, the 8th segment is only 2 wide.
> model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2),
> min.width = 5)
> fit(model, force = TRUE)
There were 50 or more warnings (use warnings() to see the first 50)
> foldChangeTable <- getRegions(model)[[1]]
> foldChangeTable[1:10,]
chromosome start stop mean count
url
1 1 51599 14941584 0.1975 7929
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A0-16430583
2 1 14944039 16878322 -0.3535 1163
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A14750611-17071750
3 1 16878364 17215511 -0.0717 163
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16844649-17249226
4 1 17217671 26830062 -0.3424 6070
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16256432-27791301
5 1 26830481 72541505 0.1856 28889
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A22259379-77112607
6 1 72541525 72583737 2.0660 45
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A72537304-72587958
7 1 72584492 101046159 0.1900 18772
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A69738325-103892326
8 1 101046857 101047369 -2.8866 2
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A101046806-101047420
9 1 101047606 150822152 0.1841 15874
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A96070151-155799607
10 1 150822331 150852863 2.6550 31
http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A150819278-150855916
I don't think the warnings are related to my question, but here they are,
anyway :
> warnings()
Warning messages:
1: In log(M, base = 2) : NaNs produced
2: In log(A, base = 2) : NaNs produced
3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... :
array has repeated maploc positions
4: In log(M, base = 2) : NaNs produced
5: In log(A, base = 2) : NaNs produced
6: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... :
array has repeated maploc positions
... ... ...
I'm using aroma.affymetrix 1.7.0 on R 2.12.0 alpha.
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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