Dear all, I stumbled upon some unexpected behaviour with cbind'ing SummarizedExperiment objects with unnamed assays:
> require(GenomicRanges) > nrows <- 5; ncols <- 4 > counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) > rowData <- GRanges("chr1", IRanges(1:nrows, 1:nrows)) > colData <- DataFrame(Treatment=1:ncols, row.names=LETTERS[1:ncols]) > sset <- SummarizedExperiment(counts, rowData=rowData, colData=colData) > sset class: SummarizedExperiment dim: 5 4 exptData(0): assays(1): '' rownames: NULL rowData metadata column names(0): colnames(4): A B C D colData names(1): Treatment > > cbind(sset, sset) dim: 5 8 exptData(0): assays(0): rownames: NULL rowData metadata column names(0): colnames(8): A B ... C1 D1 colData names(1): Treatment Upon cbind'ing, the assays in the SE object are lost. I think this is due to the fact that the cbind code matches up assays by their names. Thus, if there are no names, the code assumes that there are no assays. I guess this could be prevented by enforcing naming of assays in the SummarizedExperiment constructor. Or, the binding code could be modified to work positionally when there are no assay names, e.g., by cbind'ing the first assays across all SE objects, then the second assays, etc. Any thoughts? Regards, Aaron > sessionInfo() R Under development (unstable) (2014-12-14 r67167) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.19.42 GenomeInfoDb_1.3.13 IRanges_2.1.41 [4] S4Vectors_0.5.21 BiocGenerics_0.13.6 loaded via a namespace (and not attached): [1] XVector_0.7.4 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel