Entering edit mode
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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