
Dear Johnbosco Taybewa,

Thank you for reporting this problem. We are already working on fixing 
it in the next version which will be released within the next 
days(probably 10th Feb).

Best regards,
Günter Klambauer

On 02/07/2014 05:11 PM, Johnbosco [guest] wrote:
> I used getSegmentReadCountsFromBAM() to get a GRanges object from a list of tumor-normal bam files
> Then I used referencecn.mops(). Whenever I try to calculate integer copy numbers using calcIntegerCopyNumbers() I get an error. This error can be reproduced using the data provided by cn.mops so this might be a bug?
>
>> data(cn.mops)
>> resRef2 <- referencecn.mops (XRanges[,1], XRanges[,2])
> Normalizing...
> Starting local modeling, please be patient...
> Reference sequence:  chrA
> Starting segmentation algorithm...
> Using "fastseg" for segmentation.
>> resRef5 <- calcIntegerCopyNumbers(resRef2)
> Error in `colnames<-`(`*tmp*`, value = "S_1") :
>    length of 'dimnames' [2] not equal to array extent
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] snow_0.3-13          cn.mops_1.8.3        GenomicRanges_1.14.4
> [4] XVector_0.2.0        IRanges_1.20.6       Biobase_2.22.0
> [7] BiocGenerics_0.8.0   BiocInstaller_1.12.0
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.30.1 bitops_1.0-6      Rsamtools_1.14.2  stats4_3.0.2
> [5] tools_3.0.2       zlibbioc_1.8.0
>
> --
> Sent via the guest posting facility at bioconductor.org.


-- 
Günter Klambauer
Institute of Bioinformatics
Johannes Kepler University, Linz, Austria
http://www.bioinf.jku.at/people/klambauer/


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