[Bioc-devel] Changes to the SummarizedExperiment Class

[Peter Haverty]

There are some nice similarities in these new imaginary types.  A
"GRangesFrame" is a list of dimensionally identical things (columns) and
some row meta-data (the GRanges).  The SE-like object is similarly a list
of dimensionally like things (matrices, RleDataFrames, BigMatrix objects,
HDF5-backed things) with some row meta-data (a DataFrame or GRangesFrame).
Elegant?  Maybe they would actually be relatives in the class tree.

I wonder if this kind of thing would be easier if we had Java-style
Interfaces or duck-typing.  The "x" slot of "y" holds something that
implements this set of methods ...

Oh, and kinda apropos, the genoset class will probably go away or become an
extension to this new SE-like thing.  The extra stuff that comes along with
genoset will still be available.

Pete

____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com

On Tue, Mar 3, 2015 at 3:42 PM, Tim Triche, Jr. <tim.triche at gmail.com>
wrote:

> This.
>
> It would be damned near perfect as a return value for assays coming out of
> an object that held several such assays at several time points in a
> population, where there are both assay-wise and covariate-wise "holes" that
> could nonetheless be usefully imputed across assays.
>
>
> Statistics is the grammar of science.
> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
>
> On Tue, Mar 3, 2015 at 3:25 PM, Peter Haverty <haverty.peter at gene.com>
> wrote:
>
> > >
> > >
> > >
> > >  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.
> > >>
> > >
> > > Just impossible. As Michael mentioned back in November, they have
> > > conflicting APIs.
> >
> >
> > Maybe a new "GRangesFrame" that is a DataFrame and holds a GRanges
> > (without mcols) as an index?
> >
> >
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> >
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