[BioC] countGenomicOverlaps output

[Mete Civelek]

Hi All,

I want countGenomicOverlaps to output a count of uniquely mapping reads
within a genomic feature. Will setting the resolution parameter to 'none'
allow countGenomicOverlaps to ignore reads which map to multiple locations
in the genome? If so, countGenomicOverlaps doesn't behave the way I expect
it to. I am using the Bioconductor GenomicRanges package version 1.4.6.

Example:

library(GenomicRanges)
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='none')

I would have expected the hit count to be 0 but instead it reports it as
1/3. Am I using this function correctly?

Thanks,

Mete


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