[BioC] Weighted counts in countGenomicOverlaps

[Valerie Obenchain]

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
>
>
>
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