[Bioc-devel] Changes to the SummarizedExperiment Class

[Michael Lawrence]

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?
>
> ~G
>
> On Tue, Mar 3, 2015 at 2:37 PM, Jim Hester <james.f.hester at 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.
> >
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> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> --
> Gabriel Becker, Ph.D
> Computational Biologist
> Genentech Research
>
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>
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