[Bioc-devel] Changes to the SummarizedExperiment Class
Vincent Carey
stvjc at channing.harvard.edu
Wed Mar 4 15:40:38 CET 2015
I am a bit concerned about any major alterations to the
SummarizedExperiment API. We have
two papers and plenty of working code that use it in meaningful ways.
Effort required to keep new
formulations back-compatible as well as bug-free has to be weighed
seriously.
I agree that the name is not ideal. We are learning as we go.
Seems to make sense to start with the contracts we want the instances of a
class to satisfy. I have long felt
that X[i, j] idiom is one users and developers should be comfortable with,
even insist on, and for consistency
with matrix operations idiom, it should work in a natural way for numeric
indexing. This seems like an important
constraint. subsetBy* is a useful idiom, but it is conceivable that we
would adopt filter() for row-oriented selections
and select() for column-oriented selections. Do we have to make any
special design considerations to allow
very smooth interoperation with out-of-memory resources for certain
components for developers who want to allow this?
We should have a reasonable way to get data on what is out there, what is
used, how it is most effectively used.
What's the SE API? Is it well-adapted to requirements of DESeq2? Other
killer packages that use/don't use it?
Even getting data on the formal API for a class is not all that familiar.
And if folks are writing non-S4 interfaces (i.e., naked
functions) we have no way of identifying them. See below for one way of
discovering the API for SummarizedExperiment.
In summary, I think we have to be careful about overdesigning too early.
Getting clear on contracts seems the best
way to ensure reuse, and we really want that so that reliability is
continually assessed. My sense is that it is good
to give developers something they'll gladly extend, not necessarily reuse
directly. So we don't have to have
broad consensus on class details, but on the minimal abstraction and on
obligatory tests on its basic implementation.
> methods(class="SummarizedExperiment") # perhaps an obsolete version of
methods cataloguer by MTM
DataFrame with 76 rows and 3 columns
generic
signature package
<character>
<character> <character>
1 [ x="SummarizedExperiment", i="ANY",
j="ANY", drop="ANY" base
2 [ x="SummarizedExperiment", i="ANY",
j="missing", value="ANY" base
3 [ x="SummarizedExperiment",
i="ANY", j="missing" base
4 [<- x="SummarizedExperiment", i="ANY", j="ANY",
value="SummarizedExperiment" base
5 assay x="SummarizedExperiment",
i="character" GenomicRanges
... ...
... ...
72 updateObject
object="SummarizedExperiment" BiocGenerics
73 values
x="SummarizedExperiment" S4Vectors
74 values<-
x="SummarizedExperiment" S4Vectors
75 width
x="SummarizedExperiment" BiocGenerics
76 width<-
x="SummarizedExperiment" BiocGenerics
On Wed, Mar 4, 2015 at 8:32 AM, Hector Corrada Bravo <hcorrada at gmail.com>
wrote:
> May I advocate for 'IndexedDataFrame' or 'IndexedFrame'? 'rowIndices' can
> return whatever makes sense (GRanges, or other data structures -thinking
> taxonomy for metagenomics for example-). GRangesFrame can inherit from
> this.
>
> On Wed, Mar 4, 2015 at 3:28 AM, Hervé Pagès <hpages at fredhutch.org> wrote:
>
> > GRangesFrame is an interesting idea and I gave it some thoughts.
> >
> > There is this nice symmetry between GRanges and GRangesFrame:
> >
> > - GRanges = a naked GRanges + a DataFrame accessible via mcols()
> >
> > - GRangesFrame = a DataFrame + a naked GRanges accessible via
> > some accessor (e.g. rowRanges())
> >
> > So GRanges and GRangesFrame are equivalent in terms of what they
> > can hold, but different in terms of API: the former has the ranges
> > API as primary API and the DataFrame API on its mcols() component,
> > and the latter has the DataFrame API as primary API and the ranges
> > API on its rowRanges() component. Nice switch!
> >
> > What does this API switch bring us? A GRangesFrame object is now
> > an object that fully behaves like a DataFrame and people can also
> > perform range-based operations on its rowRanges() component.
> > Here is what I'm afraid is going to happen: people will also want
> > to be able to perform range-based operations *directly* on
> > these objects, i.e. without having to call rowRanges() first.
> > So for example when they do subsetByOverlaps(), subsetting
> > happens vertically. Also the Hits object returned by findOverlaps()
> > would contain row indices. Problem with this is that these objects
> > now start to suffer from the "dual personality syndrome". For
> > example, it's not clear anymore what their length should be.
> > Strictly speaking it should be their number of columns (that's
> > what the length of a DataFrame is), but the ranges API that
> > we're trying to put on them also makes them feel like vectors
> > along the vertical dimension so it also feels that their length
> > should be their number of rows. Same thing with 1D subsetting.
> > Why does it subset the columns and not the rows? Most people
> > are now confused.
> >
> > It's interesting to note that the same thing happens with GRanges
> > objects, but in the opposite direction: people wish they could
> > do DataFrame operations directly on them without calling mcols()
> > first. But in order to preserve the good health of GRanges objects,
> > we've not done that (except for $, a shortcut for mcols(x)$,
> > the pressure was just too strong).
> >
> > H.
> >
> >
> >
> > On 03/03/2015 04:35 PM, Michael Lawrence wrote:
> >
> >> Should be possible for the annotations to be of any type, as long as
> they
> >> satisfy a simple contract of NROW() and 2D "[". Then, you could have a
> >> DataFrame, GRanges, or whatever in there. But it would be nice to have a
> >> special class for the container with range information. The contract for
> >> the range annotation would be to have a granges() method.
> >>
> >> I agree it would be nice if there was a way with the methods package to
> >> easily assert such contracts. For example, one could define an interface
> >> with a set of generics (and optionally the relevant position in the
> >> generic
> >> signature). Then, once all of the methods have been assigned for a
> >> particular class, it is made to inherit from that contract class. There
> >> are
> >> lots of gotchas though. Not sure how useful it would be in practice.
> >>
> >>
> >> On Tue, Mar 3, 2015 at 4:07 PM, Peter Haverty <haverty.peter at gene.com>
> >> wrote:
> >>
> >> There are some nice similarities in these new imaginary types. A
> >>> "GRangesFrame" is a list of dimensionally identical things (columns)
> and
> >>> some row meta-data (the GRanges). The SE-like object is similarly a
> list
> >>> of dimensionally like things (matrices, RleDataFrames, BigMatrix
> objects,
> >>> HDF5-backed things) with some row meta-data (a DataFrame or
> >>> GRangesFrame).
> >>> Elegant? Maybe they would actually be relatives in the class tree.
> >>>
> >>> I wonder if this kind of thing would be easier if we had Java-style
> >>> Interfaces or duck-typing. The "x" slot of "y" holds something that
> >>> implements this set of methods ...
> >>>
> >>> Oh, and kinda apropos, the genoset class will probably go away or
> become
> >>> an extension to this new SE-like thing. The extra stuff that comes
> along
> >>> with genoset will still be available.
> >>>
> >>> Pete
> >>>
> >>> ____________________
> >>> Peter M. Haverty, Ph.D.
> >>> Genentech, Inc.
> >>> phaverty at gene.com
> >>>
> >>> On Tue, Mar 3, 2015 at 3:42 PM, Tim Triche, Jr. <tim.triche at gmail.com>
> >>> wrote:
> >>>
> >>> This.
> >>>>
> >>>> It would be damned near perfect as a return value for assays coming
> out
> >>>> of
> >>>> an object that held several such assays at several time points in a
> >>>> population, where there are both assay-wise and covariate-wise "holes"
> >>>> that
> >>>> could nonetheless be usefully imputed across assays.
> >>>>
> >>>>
> >>>> Statistics is the grammar of science.
> >>>> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
> >>>>
> >>>> On Tue, Mar 3, 2015 at 3:25 PM, Peter Haverty <haverty.peter at gene.com
> >
> >>>> wrote:
> >>>>
> >>>>
> >>>>>>
> >>>>>>
> >>>>>> 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
> >>>>>> conflicting APIs.
> >>>>>>
> >>>>>
> >>>>>
> >>>>> Maybe a new "GRangesFrame" that is a DataFrame and holds a GRanges
> >>>>> (without mcols) as an index?
> >>>>>
> >>>>>
> >>>>> [[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
> >>>>
> >>>>
> >>>
> >>>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> > --
> > 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
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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>
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