Hi, +1 from me, too ... I've also had a similar conversion function (data.[frame|table] <--> GRanges) in my toolbelt which I found quite useful over the years.
-steve On Sun, Oct 6, 2013 at 5:00 PM, Kasper Daniel Hansen <kasperdanielhan...@gmail.com> wrote: > 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 -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
