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

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

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