On Fri, Apr 3, 2015 at 7:32 AM, Michael Love <michaelisaiahl...@gmail.com> wrote: > hi Martin, > > I noticed with GenomicRanges 1.19.51, a new, or newly functional, > check on dimnames differing between assays.
ah, I'm still using 1.19.50, maybe that's the issue. But I'd still like to hear what the new behavior will be so I can build without error :) > > It might be convenient to add an option that assays() will take an > incoming matrix without error no matter what, even if the dimnames on > the incoming matrix are not the same as those of the > SummarizedExperiment. > > Currently, it appears if there are no dimnames on the incoming matrix, > withDimnames=FALSE allows assignment (without this arg we get an > error), but with mismatched dimnames, withDimnames=FALSE gives an > error. > > Also, the help file should probably be updated, as it seems the > argument is not actually ignored for the setter. Unless this > functionality above was unintended? > > "withDimnames: A ‘logical(1)’, indicating whether dimnames should be > applied to extracted assay elements (this argument is ignored > for the setter ‘assays<-’). Setting ‘withDimnames=FALSE’ > increases the speed and memory efficiency with which assays > are extracted." > > best, > > Mike > > ~~~~~ > > >> (se <- SummarizedExperiment(matrix(1:6, ncol=2, dimnames=list(1:3,1:2)), >> colData=DataFrame(x=1:2))) > class: SummarizedExperiment > dim: 3 2 > exptData(0): > assays(1): '' > rownames(3): 1 2 3 > rowRanges metadata column names(0): > colnames: NULL > colData names(1): x > >> assays(se)[["test"]] <- matrix(7:12, ncol=2) > Error in `assays<-`(`*tmp*`, value = <S4 object of class "SimpleList">) : > 'dimnames' differ between assay elements > Calls: assays<- -> assays<- > > # error because the incoming matrix doesn't have the same dimnames > >> assays(se, withDimnames=FALSE)[["test"]] <- matrix(7:12, ncol=2) > > # no error, as expected because withDimnames=FALSE > >> assays(se)[["test"]] <- matrix(7:12, ncol=2, dimnames=list(4:6,3:4)) > Error in `assays<-`(`*tmp*`, value = <S4 object of class "SimpleList">) : > 'dimnames' differ between assay elements > Calls: assays<- -> assays<- > > # again, mismatched dimnames, so error > >> assays(se, withDimnames=FALSE)[["test"]] <- matrix(7:12, ncol=2, >> dimnames=list(4:6,3:4)) > Error in `assays<-`(`*tmp*`, withDimnames = FALSE, value = <S4 object > of class "SimpleList">) : > 'dimnames' differ between assay elements > Calls: assays<- -> assays<- > > # error despite asking withDimnames=FALSE > >> sessionInfo() > R Under development (unstable) (2015-01-19 r67547) > Platform: x86_64-unknown-linux-gnu (64-bit) > Running under: Ubuntu 14.04.2 LTS > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices datasets utils > methods > [9] base > > other attached packages: > [1] GenomicRanges_1.19.50 GenomeInfoDb_1.3.16 IRanges_2.1.43 > [4] S4Vectors_0.5.22 BiocGenerics_0.13.10 RUnit_0.4.28 > [7] devtools_1.7.0 knitr_1.9 BiocInstaller_1.17.7 > > loaded via a namespace (and not attached): > [1] evaluate_0.5.5 formatR_1.0 stringr_0.6.2 tools_3.2.0 XVector_0.7.4 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
