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.

Michael

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