[Bioc-devel] Changes to the SummarizedExperiment Class

Gabe Becker becker.gabe at gene.com
Tue Mar 3 23:44:20 CET 2015

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?


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.
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Gabriel Becker, Ph.D
Computational Biologist
Genentech Research

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