[BioC] DNAcopy segment() Infinite Loop

[SeshanV at mskcc.org]

There is something weird in your data set. Of the 154005 values there are
137109 unique ones. Oddly there are 16335 that have the same value.

> table(table(cn$Fold.Change))

     1      2      3      4      5      9  16335
135779    883     31      3      1      1      1

Those 16335 repeated values give several contiguous stretches of duplicated
values, some very long (a stretch of 921 at the start of chr13), which are
bypassing various sanity checks in the code.

Venkat

On 6/23/11 1:00 AM, "Dario Strbenac" <D.Strbenac at garvan.org.au> wrote:

> Hello,
> 
> I have some data that I'm segmenting with DNAcopy and the processing enters an
> infinite loop when it gets to chr13. It's worked for me previously on other
> datasets, so this could be one of those problems that is hard to track down
> because it only happens on a certain dataset. But I am hopeful that the
> maintainer might have the intuition and experience to uncover the cause of it.
> 
> Here is a minimal and reproducible example :
> 
> library(DNAcopy)
> download.file("http://129.94.136.7/file_dump/dario/CNobjects.RData",
> "./CNobjects.RData") # 3.2 MB
> load("CNobjects.RData") # objects 'cn' and 'wts'
> segment(cn, weights = wts, verbose = 3)
> 
> My session is :
> 
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] DNAcopy_1.26.0
> 
> loaded via a namespace (and not attached):
> [1] tools_2.13.0
> 
> 
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
> 

-- 
Venkatraman E. Seshan, Ph.D. | Attending Biostatistician
Director of Biostatistics Computer-Intensive Support Services
Department of Epidemiology and Biostatistics | MSKCC
307 E 63rd St 3rd Floor | New York, NY 10065
Phone: 646-735-8126 | Fax: 646-735-0010



 
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