[BioC] summarizeOverlaps: ambiguous method dispatch

[Martin Morgan]

On 05/18/2013 04:38 PM, Michael Lawrence wrote:
> Entering this code:
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> library(LungCancerLines)
> exons <- exons(TxDb.Hsapiens.UCSC.hg19.knownGene, vals = list(gene_id =
> "7157"))
> counts <- summarizeOverlaps(exons, LungCancerBamFiles())
>
> Yields:
>
> Note: method with signature 'GAlignments#Vector' chosen for function
> 'countOverlaps',
>   target signature 'GAlignments#GRanges'.
>   "Vector#GenomicRanges" would also be valid
> Note: method with signature 'GAlignments#Vector' chosen for function
> 'countOverlaps',
>   target signature 'GAlignments#GRanges'.
>   "Vector#GenomicRanges" would also be valid
>
> While this is apparently harmless, a couple of questions:
>
> - What is the rationale for defining countOverlaps methods on 'Vector'? If
> this is a simple wrapper, why not go all the way to ANY?
>
> - Would it be feasible to avoid these Notes (which probably unnecessarily
> worry the user), for example by defining specific methods for GenomicRanges
> and GRangesList? I realize that dual dispatch is inherently prone to
> ambiguities, but some brute-forcing might be worth the effort.

Yes, this will get addressed, thanks for the heads up. Martin

>
> Michael
>
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>
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