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

[Michael Love]

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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>