[Bioc-devel] RangedSummarizedExperiment

[Kasper Daniel Hansen]

I agree 100%: It would be wonderful to have a roadmap and (perhaps) some
high level discussion of what should be done for various things.  Things
are breaking right and left and we don't want to have to deal with this
again in 6 months, so why don't we make sure the design has been looked at
with more eyes.

For example, we really, really need to have colnames on the assay matrices.

Kasper

On Thu, Jun 18, 2015 at 1:48 PM, Tim Triche, Jr. <tim.triche at gmail.com>
wrote:

> Hey since the refactoring is already breaking stuff willy nilly, can I
> make a few suggestions?
>
> 1) please for the love of all that is holy have backwards compatible
> methods for RSEs.  It's excruciating to have RSE as the target class,
> supporting RELEASE users with SE, and have to do endless duck typing
> nonsense or else have a bunch of new generics.
>
> 2) please investigate some sort of "overlay" approach that would allow for
> accordion-style bundling/unbundling of transcripts, regions, compartments
> etc.  the reason for this will become ever more obvious, but now that I
> have students, I don't want to explain why everything seems to derive from
> a pre-ASE, pre-intronretention, pre-graphreference mindset of 20 years
> ago.  If you're going to break stuff, how about we break it real good and
> make things going forward flexible so as to eventually get it "right
> enough" (NOT "perfect" or "right" but "close enough for government work"
> and "close enough to work out of core")
>
> 3) I'll write patches ( you may not want to actually accept them, but I'll
> write 'em just the same ) when the urge moves me, but if some sort of a
> 30000' summary of the desired end product (along with deficiencies of the
> current SE) were readily available, it might help avoid a "second system
> effect".  The original SE was very good, fixing almost everything that
> sucked about the battle-tested ExpressionSet.  The new RSE has the great
> feature of automatically putting transcripts about where they belong if I
> point it at, say, a GEO GSE.  I assume that with things like Kallisto we
> can eventually do the same with arbitrary SRA experiments (there's a cute
> hack we are pushing in BaseSpace to make this happen already). But without
> a roadmap, it's tougher for people to see what needs to NOT be done, and
> that's really important.  What belongs in the base class, and what in a
> subclass?  This is not unimportant.
>
> All of the above said, SE was great and RSE is already better in some
> respects. But with a clear roadmap and more input, I bet it (and a tight
> clean definition of what it is and isn't supposed to do) would be better-er.
>
> (Steps off soapbox)
>
> --t
>
> > On Jun 18, 2015, at 10:25 AM, Hervé Pagès <hpages at fredhutch.org> wrote:
> >
> > 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.
> >
> > H.
> >
> >>
> >> Thanks,
> >> E.
> >
> > --
> > Hervé Pagès
> >
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpages at fredhutch.org
> > Phone:  (206) 667-5791
> > Fax:    (206) 667-1319
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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