Done in SummarizedExperiment 0.3.2. Thanks for the feedback, H.
On 06/29/2015 10:26 PM, Hervé Pagès wrote:
Hi Nico, It seems reasonable indeed to support rowRanges<- on SummarizedExperiment0. It might be a little bit surprising for the user that the setter changes the class of the object but it looks like a perfectly legit situation for doing so here. Also there are some precedents: > x <- 1:5 > x[1] <- "a" > x [1] "a" "2" "3" "4" "5" and: library(Biostrings) dna <- DNAString("GGATTAAA") class(dna) # DNAString masks(dna) <- Mask(length(dna), 2, 5) class(dna) # MaskedDNAString I'll add this, unless someone has a better idea? Thanks, H. On 06/29/2015 03:13 AM, Nicolas Delhomme wrote:Hej alla! In the simpleRNASeq function of the easyRNASeq package, I start by instantiating a SummarizedExperiment object not initially providing the rowRanges. This results in the creation of an object of the class SummarizedExperiment0. When later, once I have validated the annotation, I try to extend the rowRanges of my SummarizedExperiment object, I get an error message that "rowRanges<-" is not implemented for signature "SummarizedExperiment0, GRangesList". I'm now wondering if this has been omitted on purpose for SummarizedExperiment0 objects or is not yet implemented. The reason I'm wondering is because there is the possibility to cast a SummarizedExperiment0 object as a RangedSummarizedExperiment (which is my current work-around), but I'm wondering if that's the best way to go. I don't have access to my Rsession right now, so no sessionInfo(), but I'm using R3.2.1 on OSX 10.10.3 (Yosemite), and the latest devel packages (updated today; SummarizedExperiment version is 0.3.0). Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme, PhD The Street Lab Department of Plant Physiology Umeå Plant Science Center Tel: +46 90 786 5478 Email: nicolas.delho...@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --------------------------------------------------------------- _______________________________________________ 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
