If it makes genosets coercible into SEs then I'm all for the change and its permanence
--t > On Mar 25, 2014, at 9:31 AM, Peter Haverty <haverty.pe...@gene.com> wrote: > > One benefit of having dimnames on assays would be that one could use > DataFrames as assays, like in eSet. My genoset class is becoming more and > more like SummarizedExperiment. The dimname issues prevent me from > switching entirely from eSet to SummarizedExperiment. > > I think that keeping only one copy of dimnames is a great feature, if a bit > dangerous. My typical object has ~6 BigMatrix and/or DataFrame of Rle > objects as assays, so the rownames actually make up a considerable portion > of the object size. (My typical dataset is 2.5M rows by 1k samples). I've > been moving towards keeping a single dimnames copy just to improve RData > load times. > > I think that assays should be required to have dimnames when they are added > to a SummarizedExperiment. These dimnames should be checked for equality > with the dimnames of the SE in the setter function. > > Perhaps with the recent (R 3.1) improvements in shallow/lazy copying and > reference counting, adding dimnames to outgoing assays will be less of a > performance hit. > > I also like the compromise I have seen elsewhere, where the colnames are > always retained on assays, but only one rownames copy is kept. Colnames > are typically small and getting them wrong often makes for silent, but > catastrophic errors. > > Pete > > ____________________ > Peter M. Haverty, Ph.D. > Genentech, Inc. > phave...@gene.com > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
