[BioC] subdivideGRanges() to a given number of ranges

[Valerie Obenchain]

Hi Dolev,

I am copying the maintainer of exomeCopy which is the package 
subdivideGRanges() comes from. Please provide a small reproducable 
example of the problem you are having (i.e., a few lines of code that 
someone else can run to get the same error). This makes it easier for 
others to help.

Valerie

On 09/06/12 04:39, d r wrote:
> Hello
>
> I have a GRanges object representing CpG islands, that I want to subdivide
> so that each island will be represented by 10 ranges of equal width.
>
> To do this, I created a vector containing the widths of the islands divided
> by ten:
>
> swidth<-as.integer(width(islandshg19)/10)
>
>
>
> and then called subdivideGRanges():
>
>
> islandshg19<-subdivideGRanges(islandshg19, subsize=as.integer(width/10))
>
>
> and got a multitude of warnings.
>
>
> This approach did work when I tried it on a GRanges object containing a
> single range, and a width vector of length 1. When I tried to extend the
> sample to include two objetcs, I got these warning message:
>
> 1: In if (widths[i]<  2 * subsize) { ... :
>
>    the condition has length>  1 and only the first element will be used
>
> 2: In if (width<  2 * subsize) { ... :
>
>    the condition has length>  1 and only the first element will be used
>
> 3: In 0:(nchunks - 1) : numerical expression has 2 elements: only the first used
>
>
>
> Which makes me think that the problem may be related to assigning the right
> subszie to the the rigth range.
>
> Does anyone have an idea how to do that?
>
> Thanks in advance
>
> Dolev Rahat
>
>
>
> sessionInfo(if required):
>
> R version 2.15.1 (2012-06-22)
>
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
>
>
> locale:
>
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
>
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
> other attached packages:
>
>   [1] exomeCopy_1.2.0      Rsamtools_1.8.6      Biostrings_2.24.1
> rtracklayer_1.16.3   taRifx_1.0.4         reshape2_1.2.1
> plyr_1.7.1
>
>   [8] XML_3.9-4.1          GenomicRanges_1.9.54 IRanges_1.15.40
> BiocGenerics_0.3.1   BiocInstaller_1.4.7
>
>
>
> loaded via a namespace (and not attached):
>
> [1] bitops_1.0-4.1  BSgenome_1.25.7 RCurl_1.91-1.1  stats4_2.15.1
> stringr_0.6.1   tools_2.15.1    zlibbioc_1.2.0
>
> 	[[alternative HTML version deleted]]
>
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