[Bioc-devel] what is SummarizedExperiment a Vector of?

[Michael Lawrence]

On Tue, Dec 15, 2015 at 2:15 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> SummarizedExperiment has long been supporting unidimensional subsetting
> which was subsetting by row. However the length of any SE object was
> always considered to be 1 which was confusing. The new implementation
> still supports unidimensional subsetting but now the length of an
> object is its number of rows.
>

Thanks for the clarification. It's not totally obvious that an SE
should be row-oriented. It almost acts like an extension of GRanges.
Water under the bridge at this point, I guess.

> H.
>
>
> On 12/15/2015 11:31 AM, Vincent Carey wrote:
>>
>> It seems worthy of discussion.  My outlook, surely naive, is that
>> SummarizedExperiment is Vector if it can answer all these meaningfully
>>
>>> methods(class="Vector")
>>
>>
>>   [1] !=                [                 [<-               %in%
>>
>>   [5] <                 <=                ==                >
>>
>>   [9] >=                aggregate         anyNA             append
>>
>> [13] as.character      as.complex        as.data.frame     as.env
>>
>> [17] as.integer        as.list           as.logical        as.numeric
>>
>> [21] as.raw            by                coerce            compare
>>
>> [25] countOverlaps     duplicated        elementMetadata
>> elementMetadata<-
>>
>> [29] eval              expand            expand.grid       extractROWS
>>
>> [33] findOverlaps      head              high2low          length
>>
>> [37] lengths           match             mcols             mcols<-
>>
>> [41] metadata          metadata<-        mstack            NROW
>>
>> [45] overlapsAny       parallelSlotNames rank              relist
>>
>> [49] rename            rep               rep.int           replaceROWS
>>
>> [53] rev               ROWNAMES          seqlevelsInUse    shiftApply
>>
>> [57] showAsCell        sort              split             split<-
>>
>> [61] subset            subsetByOverlaps  table             tail
>>
>> [65] tapply            unique            values            values<-
>>
>> [69] window            window<-          with              xtabs
>>
>> [73] xtfrm
>>
>>
>> it seems to me that it would be most natural to regard it as a Vector of
>> features.  But I don't know if I give the right principle or if it should
>> be detached from Vector for some reason.
>>
>> On Tue, Dec 15, 2015 at 2:21 PM, Michael Lawrence
>> <lawrence.michael at gene.com
>>>
>>> wrote:
>>
>>
>>> It totally makes sense for a matrix to be a vector. But it's a whole
>>> other thing for a SummarizedExperiment to be a Vector. It could be
>>> made to work, but I sort of doubt there is much consistency right now.
>>> Perhaps I'm wrong.
>>>
>>> On Tue, Dec 15, 2015 at 11:15 AM, Vincent Carey
>>> <stvjc at channing.harvard.edu> wrote:
>>>>
>>>> perhaps the answer has to reflect
>>>>
>>>>> is(matrix(), "vector")
>>>>
>>>>
>>>> [1] TRUE
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Dec 15, 2015 at 2:05 PM, Michael Lawrence
>>>> <lawrence.michael at gene.com> wrote:
>>>>>
>>>>>
>>>>> Saw that SummarizedExperiment(0) derives from Vector. What exactly is
>>>>> it a Vector of? Features? Measurements? It is rectangular, like a
>>>>> matrix, but does it support unidimensional subscripts? Sort of
>>>>> confusing.
>>>>>
>>>>> Thanks for clarifying,
>>>>> Michael
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>>
>>>
>>
>>         [[alternative HTML version deleted]]
>>
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>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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>
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