[Bioc-devel] Changes to the SummarizedExperiment Class

[Peter Haverty]

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.
phaverty at gene.com

On Tue, Mar 3, 2015 at 2:57 PM, Michael Lawrence <lawrence.michael at 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.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.
> > >
> > >         [[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]]
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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