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

[Vincent Carey]

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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