hi Dolev,

Yes this function was designed to accept a single value for 'subsize', 
which is the desired width of the output ranges.  It is not possible to 
use this function to create x subdivided ranges for each range in the input.

cheers

Mike

On 9/6/12 8:33 PM, d r wrote:
> Thank you Mike and Valarie,
>
> Just to be sure I understood you clearly: I understand there is no 
> possibilty to use  subdivideGRanges() to split a GRanges to a given 
> number of elements.
> If I understood you correctly, it is also not possible to read a 
> vector into the subsize argument. is taht true or is ther some 
> possibilty to do that?
>
> thanks again
> Dolev
>
> On Thu, Sep 6, 2012 at 5:17 PM, Michael Love <love@molgen.mpg.de 
> <mailto:love@molgen.mpg.de>> wrote:
>
>     Hi Dolev,
>
>     The subdivideGRanges() function cannot accomplish this task.
>
>     from the manual:
>
>     "Takes an input GRanges object and, splits each range into
>     multiple ranges of nearly equal width. For an input range of width
>     w and subdividing size s, it will subdivide the range into
>     max(1,floor(w/s)) nearly equal width ranges."
>
>     So the function tries to keep the widths of the subdivided ranges
>     around s basepairs, rather than keeping the number of subdivided
>     ranges constant.
>
>     I will include a more helpful error message if a vector is
>     provided for the subsize argument.
>
>     cheers,
>
>     Mike
>
>
>
>     On 09/06/12 16:02, Valerie Obenchain wrote:
>
>         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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>
>
>
>


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