[Bioc-devel] Changes to the SummarizedExperiment Class

[Hervé Pagès]

On 03/03/2015 03:06 PM, Peter Haverty wrote:
> I'd like to see a basic class that takes a DataFrame and a sub-class that
> takes a GRanges.

Yes.

> 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.

>
> 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?

We actually need 2 names: 1 for the parent class, 1 for the child. I'm
starting to think that introducing 2 new names would maybe make the
migration a little bit easier, especially since the plan is to move the
"refactored SummarizedExperiment" to its own package. With 2 new names
we can start the new package, implement the 2 new classes in it, and
have the old SummarizedExperiment (in GenomicRanges) and the 2 new
classes peacefully cohabit during the time of the migration.

Cheers,
H.

>
>   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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>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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>>
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>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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