This is a convenience function, which provably has saved tons of time for me and others. I get lots of data from various excel/cvs files lying around various places, and these files _always_ have a clear path to a GRanges. Perhaps you never have to deal with this kind of data, but we are a few experienced users who find it extremely handy and would like it to be in a more centralized place.
On Sun, Oct 6, 2013 at 4:26 PM, Michael Lawrence <lawrence.mich...@gene.com>wrote: > 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
