[Bioc-devel] Changes to the SummarizedExperiment Class
lawrence.michael at gene.com
Tue Mar 3 23:57:01 CET 2015
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.gabe at 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?
> On Tue, Mar 3, 2015 at 2:37 PM, Jim Hester <james.f.hester at gmail.com>
> > Motivated by the discussion thread from November (https://stat.ethz.ch/
> > pipermail/bioc-devel/2014-November/006686.html) the Bioconductor core
> > is planning on making changes to the SummarizedExperiment class. Our end
> > goal is to allow the @rowData slot to become more flexible and hold
> > 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
> > 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
> > any assistance with the transition.
> > [[alternative HTML version deleted]]
> > _______________________________________________
> > Bioc-devel at 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 at r-project.org mailing list
[[alternative HTML version deleted]]
More information about the Bioc-devel