On 12/15/2015 03:13 PM, Michael Lawrence wrote:
On Tue, Dec 15, 2015 at 2:15 PM, Hervé Pagès <hpa...@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.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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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