[BioC] Weighted counts in countGenomicOverlaps

[Valerie Obenchain]

Mete,

The bug is now fixed in the devel trunk (version 1.5.5) and the release 
branch (version 1.4.2). It will be a day before the new package versions 
propagate through the build system and are available through biocLite. 
If you want to retrieve them directly they are available via svn at

release :
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/GenomicRanges

devel :
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges


I've included an additional example on the man page for 
countGenomicOverlaps illustrating the handling of split reads. Let me 
know if you run into other problems.

Take care,
Valerie


On 04/26/2011 03:56 PM, Valerie Obenchain wrote:
> Hi Mete,
>
> Yes, you are using the function correctly and you have found a bug. 
> I'll let you know as soon as it's fixed.
>
> Thanks,
> Valerie
>
>
> On 04/25/2011 04:38 PM, Mete Civelek wrote:
>> Hi All,
>>
>> I want countGenomicOverlaps to output a weighted hit count such that 
>> when a
>> read maps to, for example four loci, a feature at one of those loci 
>> would
>> get 1/4th of a count from that read.
>> At the moment, countGenomicOverlaps doesn't behave the way I expect 
>> it to.
>>
>> Consider this example:
>>
>> subj = GRangesList(feature1=GRanges(seq='1', IRanges(10,30), 
>> strand='+'))
>> qry = GRangesList(read1=GRanges(seq='1', 
>> IRanges(c(10,60,100),c(20,70,110)),
>> strand='+'))
>> countGenomicOverlaps(qry, subj, resolution='divide')
>>
>> I would have expected the hit count to be 1/3 but instead it reports 
>> it as
>> 1/2. Am I using this function correctly?
>>
>> My sessioninfo is:
>>
>>
>> R version 2.12.2 (2011-02-25)
>> Platform: x86_64-unknown-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=C              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] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] GenomicRanges_1.4.0 IRanges_1.10.0
>>
>>
>>
>> IMPORTANT WARNING:  This email (and any attachments) is ...{{dropped:9}}
>>
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