I'd like to see a basic class that takes a DataFrame and a sub-class that takes a GRanges. 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.
While the hood is up, can we try some different names? SummarizedExperiment never seemed like a great fit to me because it doesn't necessarily contain experiments or summaries thereof. It's a collection of like-sized rectangular things with metadata on the two dimensions. Maybe the name could reflect what it holds rather than a common use case? AnnotatedMatrixList? Anyway, I'm excited to see a version on the way that takes a DataFrame as rowData. I'm glad you guys are working on that. Regards, Pete ____________________ Peter M. Haverty, Ph.D. Genentech, Inc. phave...@gene.com On Tue, Mar 3, 2015 at 2:57 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > Seems like rowData could be made to work universallly through coercion. > rowRanges would not, however, and one would like a convenient mechanism to > condition on whether range information is available. One way is to > introduce a new class and rely on dispatch. But that adds complexity. > > On Tue, Mar 3, 2015 at 2:44 PM, Gabe Becker <becker.g...@gene.com> wrote: > > > Jim et al., > > > > Why have two accessors (rowRanges, rowData), each of which are less > > flexible than the underlying structure and thus will fail (return NULL? > or > > GRanges()/DataFrame() ?) in some proportion of valid objects? > > > > ~G > > > > On Tue, Mar 3, 2015 at 2:37 PM, Jim Hester <james.f.hes...@gmail.com> > > wrote: > > > > > Motivated by the discussion thread from November ( > https://stat.ethz.ch/ > > > pipermail/bioc-devel/2014-November/006686.html) the Bioconductor core > > team > > > is planning on making changes to the SummarizedExperiment class. Our > end > > > goal is to allow the @rowData slot to become more flexible and hold > > either > > > a DataFrame or GRanges type object. > > > > > > To this end we have currently deprecated the current rowData accessor > in > > > favor of a rowRanges accessor. This change has resulted in a few > broken > > > builds in devel, which we are in the process of fixing now. We will > > > contact any package authors directly if needed for this migration. > > > > > > The rowData accessor will be deprecated in this release, however > > eventually > > > the plan is to re-purpose this function to serve as an accessor for > > > DataFrame data on the rows. > > > > > > Please let us know if you have any questions with the above and if you > > need > > > any assistance with the transition. > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > > > -- > > Gabriel Becker, Ph.D > > Computational Biologist > > Genentech Research > > > > [[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