On 12/23/2012 05:19 PM, Jesper Gådin wrote:
Yes thanks that is probably the reason why it is missing from
GenomicRanges. Noticed that it was in IRanges and had already put it in the
import, but forgot to also put in my export... After I put it in exports it
works as intended.
actually, GenomicRanges 1.11.20 defines new methods on subsetByOverlaps, and so
has (not literally, but in effect)
importFrom(IRanges, subsetByOverlaps)
so that the methods are associated with the correct generic, and
exportMethods(subsetByOverlaps)
so that the new methods (and generic) are available to the end user.
Not sure what your use case is, but if you were _using_ this method in your
package you would say
importFrom(GenomicRanges, subsetByOverlaps)
and likely have Imports: GenomicRanges in the DESCRIPTION file, whereas if you
were implementing a new method you'd say
importFrom(IRanges, subsetByOverlaps)
exportMethods(subsetByOverlaps)
and have at least Imports: IRanges in the DESCRIPTION file (but likely Depends:
GenomicRanges or Depends: IRanges, as it might be reasonable for the user to
have access to functionality from these packages when using your package).
I think subsetByOverlaps methods should have been exported in the release
version of GRanges (1.10.5) but were not.
Also, in passing (and probably obvious from the last couple of responses), since
you're developing a package it makes sense to track the devel branch of R and
Bioconductor. That way, your package will be ready for use when the new R / Bioc
release come out in a few months.
Martin
Jesper
On Mon, Dec 24, 2012 at 1:57 AM, Tim Triche, Jr. <tim.tri...@gmail.com>wrote:
that's probably because it is exported from IRanges
On Sun, Dec 23, 2012 at 4:19 PM, Jesper Gådin <jesper.ga...@gmail.com>wrote:
Hey,
I have noticed that subsetByOverlaps is not exported in GenomicRanges
NAMESPACE. Would be nice if someone could put it in :)
/Jesper
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