There are some nice similarities in these new imaginary types. A "GRangesFrame" is a list of dimensionally identical things (columns) and some row meta-data (the GRanges). The SE-like object is similarly a list of dimensionally like things (matrices, RleDataFrames, BigMatrix objects, HDF5-backed things) with some row meta-data (a DataFrame or GRangesFrame). Elegant? Maybe they would actually be relatives in the class tree.
I wonder if this kind of thing would be easier if we had Java-style Interfaces or duck-typing. The "x" slot of "y" holds something that implements this set of methods ... Oh, and kinda apropos, the genoset class will probably go away or become an extension to this new SE-like thing. The extra stuff that comes along with genoset will still be available. Pete ____________________ Peter M. Haverty, Ph.D. Genentech, Inc. phave...@gene.com On Tue, Mar 3, 2015 at 3:42 PM, Tim Triche, Jr. <tim.tri...@gmail.com> wrote: > This. > > It would be damned near perfect as a return value for assays coming out of > an object that held several such assays at several time points in a > population, where there are both assay-wise and covariate-wise "holes" that > could nonetheless be usefully imputed across assays. > > > Statistics is the grammar of science. > Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science> > > On Tue, Mar 3, 2015 at 3:25 PM, Peter Haverty <haverty.pe...@gene.com> > wrote: > > > > > > > > > > > > > I still think GRanges should be a subclass of DataFrame, > > >> which would make this easy, but I don't seem to be winning that > > argument. > > >> > > > > > > Just impossible. As Michael mentioned back in November, they have > > > conflicting APIs. > > > > > > Maybe a new "GRangesFrame" that is a DataFrame and holds a GRanges > > (without mcols) as an index? > > > > > > [[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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
