[Bioc-devel] Changes to the SummarizedExperiment Class
hpages at fredhutch.org
Wed Mar 4 00:16:33 CET 2015
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.
> 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
> 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?
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.
> 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.
> 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>
>> 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?
>>> 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 (
>>>> pipermail/bioc-devel/2014-November/006686.html) the Bioconductor core
>>>> is planning on making changes to the SummarizedExperiment class. Our
>>>> 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
>>>> favor of a rowRanges accessor. This change has resulted in a few
>>>> 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
>>> Gabriel Becker, Ph.D
>>> Computational Biologist
>>> Genentech Research
>>> [[alternative HTML version deleted]]
>>> Bioc-devel at r-project.org mailing list
>> [[alternative HTML version deleted]]
>> Bioc-devel at r-project.org mailing list
> [[alternative HTML version deleted]]
> Bioc-devel at r-project.org mailing list
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