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.mich...@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
<st...@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.mich...@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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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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