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 < kasperdanielhan...@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 < > kasperdanielhan...@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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
