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

[Hervé Pagès]

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.

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
>>>
>>>
>>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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