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. 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 >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>> >>>> >>>> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
