[BioC] Weighted counts in countGenomicOverlaps

[Mete Civelek]

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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