[Bioc-devel] Changes to the SummarizedExperiment Class
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 (
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]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel