[Bioc-devel] Changes to the SummarizedExperiment Class

Wed Mar 4 18:38:12 CET 2015

I think we need to make sure that there are enough benefits of something
like GRangesFrame before we introduce yet another complicated and
overlapping data structure into the framework. Prior to summarization, the
ranges seem primary, after summarization, it may often make sense for them
to be secondary. But I'm just not sure what we gain from a new data
structure.

On Wed, Mar 4, 2015 at 12:28 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]]
>>>>>
>>>>> _______________________________________________
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>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>>
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>>>>
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>>>>
>>>>
>>>
>>>
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>>
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>>
>>
> --
> 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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