I'm still unconvinced that there is an obvious, general path from
data.frame -> GRanges. It's usually easy enough to just call GRanges(),
often of the pattern with(df, GRanges(...)). Moreover, it's unusual for me
to encounter genomic data in data.frames.




On Sun, Oct 6, 2013 at 8:37 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> Also, it goes without saying that I am happy to provide a patch for
> GenomicRanges, and check that it passes R CMD check, to minimize the work
> of the maintainer.
>
> Kasper
>
>
> On Sun, Oct 6, 2013 at 9:28 AM, Kasper Daniel Hansen <
> kasperdanielhansen@gmail.com> wrote:
>
> > bsseq::data.frame2GRanges does the obvious step of converting a
> data.frame
> > to GRanges.  It has a couple of bells and whistles where strand can be
> > ignored and additional columns (apart from genomic location) may be
> ignore
> > in the output object.
> >
> > I (and now quite a few other people) use this function almost every day.
> >  I have seen other implementations in other packages, suggesting this is
> > not just something I (we) use.
> >
> > I suggests adding this function to GenomicRanges.  I am happy to support
> > it going forward.
> >
> > Using this function we could also add an as(x, "GRanges") method for
> > x=data.frame, but I still suggest keeping the basic function for the
> > extended functionality it provides.
> >
> > Best,
> > Kasper
> >
>
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