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

[Hervé Pagès]

On 12/15/2015 03:13 PM, Michael Lawrence wrote:
> 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.

Not quite. The new SummarizedExperiment has no GRanges component.

H.

> 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]]
>>>
>>> _______________________________________________
>>> 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

-- 
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