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
