Thanks for the quick action :-) 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 --------------------------------------------------------------- > On 30 Jun 2015, at 07:56, Hervé Pagès <hpa...@fredhutch.org> wrote: > > 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