so as a simple experiment, I did the following: library(GenomicRanges) bar <- matrix(rnorm(100), ncol=10) colnames(bar) <- as.character(1:10) rownames(bar) <- letters[1:10] foo <- SummarizedExperiment(assays=list(bar=bar))
rowData(foo) ## GRangesList object of length 10: ## $a ## GRanges object with 0 ranges and 0 metadata columns: ## seqnames ranges strand ## <Rle> <IRanges> <Rle> ## ## $b ## GRanges object with 0 ranges and 0 metadata columns: ## seqnames ranges strand ## ## $c ## GRanges object with 0 ranges and 0 metadata columns: ## seqnames ranges strand ## ## ... ## <7 more elements> colData(foo) ## DataFrame with 10 rows and 0 columns This got me to thinking, why not have an emptyRanges class, or else the ability to index a bunch of NULL ranges without a lot of hoohah? The defaults mostly do what they're supposed to; why not have a compact representation of empty rowData as for empty colData (i.e., a DataFrame with 0 rows)? Or is a GRangesList of empty GRanges as compact as it is practicable to get for this purpose? Just pondering what the lowest-impact solution to the problem at hand might be. Statistics is the grammar of science. Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science> On Wed, Nov 26, 2014 at 9:07 AM, Peter Haverty <haverty.pe...@gene.com> wrote: > Hi all, > > I believe there is a strong need for an object that organizes a collection > of rectangular data (matrices, etc.) with metadata on the rows and > columns. Can SummarizedExperiment inherit from something simpler that has > a DataFrame as rowData? (I believe GenomicRanges should inherit from > DataTable, rather than Vector, and subset as x[i,j], but maybe that's > getting a bit off topic.) I often see people stuffing arbitrary data into > an ExpressionSet and calling one of the assays "exprs" as a work-around. > > Regards, > > Pete > > ____________________ > Peter M. Haverty, Ph.D. > Genentech, Inc. > phave...@gene.com > > On Wed, Nov 26, 2014 at 7:19 AM, Laurent Gatto <lg...@cam.ac.uk> wrote: > > > > > On 26 November 2014 14:59, Wolfgang Huber wrote: > > > > > A colleague and I are designing a package for quantitative proteomics > > > data, and we are debating whether to base it on the > > > SummarizedExperiment or the ExpressionSet class. > > > > > > There is no immediate use for the ranges aspect of > > > SummarizedExperiment, so that would have to be carried around with > > > NAs, and this is a parsimony argument for using ExpressionSet > > > instead. OTOH, the interface of SummarizedExperiment is cleaner, its > > > code more modern and more likely to be updated, and users of the > > > Bioconductor project are likely to benefit from having to deal with a > > > single interface that works the same or similarly across packages, > > > rather than a variety of formats; which argues that new packages > > > should converge towards SummarizedExperiment('s interface). > > > > > > Are there any pertinent insights from this group? > > > > Instead of ExpressionSet, you could use MSnbase::MSnSet, which is > > essentially an ExpressionSet for quantitative proteomics (i.e it has a > > MIAPE slot, instead of MIAME for example). > > > > Ideally, a SummarizedExperiment for proteomics would use peptide/protein > > ranges, which is in the pipeline, as far as I am concerned. When that > > becomes available, there should be infrastructure to coerce and MSnSet > > (and/or other relevant data) into an SummarizedExperiment. > > > > Hope this helps. > > > > Best wishes, > > > > Laurent > > > > > Thanks and best wishes > > > Wolfgang > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > > Laurent Gatto > > http://cpu.sysbiol.cam.ac.uk/ > > > > _______________________________________________ > > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
