[Bioc-devel] RangedSummarizedExperiment

Hervé Pagès hpages at fredhutch.org
Thu Jun 18 19:25:13 CEST 2015

Hi Elena,

Sorry for the inconvenience caused by the refactoring of
SummarizedExperiment objects.

On 06/18/2015 03:41 AM, Elena Grassi wrote:
> Hello,
> I'm writing as long as I am struggling a bit to keep the pace of
> RangedSummarizedExperiment in my package roar, whose main class
> contains RangedSummarizedExperiment to hold some of the data.
> Sometimes the developers fix issues for me but I would like to ease
> their work as much as possible but for example today I stumbled upon
> this:
> http://bioconductor.org/checkResults/devel/bioc-LATEST/roar/zin1-buildsrc.html
> that is related to the fact that I build a RoarDataset object without
> rowRanges, colData etc at the beginning of the analysis and I fill
> them later.
> My questions are:
> - apart from looking around the svn logs and source code to understand
> what's going on have I missed some mail here or other information
> about the roadmap for what will come for SummarizedExperiment?

A new class, SummarizedExperiment0, was introduced for representing
"degraded" RangedSummarizedExperiment objects, that is, objects with
no rowRanges component.

So RangedSummarizedExperiment now derives from SummarizedExperiment0,
which in turn derives from Vector. As a consequence of deriving from
Vector, these objects now have a length (length(x) = nrow(x)) and can
have names (names(x) = rownames(x)).

Another consequence of these changes is that the internal representation
of RangedSummarizedExperiment objects has changed so serialized
instances need to be updated and re-serialized. Also packages that
define classes that extend RangedSummarizedExperiment (like roar)
might need some tweaks. I'm in the process of re-serializing
RangedSummarizedExperiment objects and fixing the packages affected
by these changes (should be done before the end of the week).

Note that SummarizedExperiment0 might not be the definitive name for
this class but we can't use the "SummarizedExperiment" name for this
until the old SummarizedExperiment class defined in GenomicRanges is
gone (i.e. not before BioC 3.3).

> - it would be better to avoid extending such a class and instead
> simply having another slot to avoid such initializations issues?

Not sure I understand what you're asking exactly. Can you provide
more details?

Thanks for your patience and sorry again for the inconvenience.


> Thanks,
> E.

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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