Fantastic, thanks Herve. On Tue, Jan 5, 2016 at 1:32 AM, Hervé Pagès <hpa...@fredhutch.org> wrote:
> This is fixed in S4Vectors release (0.8.6) and devel (0.9.16). > > Cheers, > H. > > > On 01/04/2016 11:52 AM, Hervé Pagès wrote: > >> Hi Malcolm, >> >> Thanks for reporting this. Will fix. >> >> H. >> >> On 01/04/2016 10:53 AM, Malcolm Perry wrote: >> >>> Hello, >>> >>> A recent question on the support site ( >>> https://support.bioconductor.org/p/76430/#76460) shows that the mcols >>> assignment in GRanges (and perhaps others) is subtly different from >>> classes >>> that purely inherit from Vector (such as GenomicInteractions in the >>> example), as the GRanges method will implicitly convert a data.frame >>> object >>> to a "DataFrame". >>> >>> Is it possible for Vector to have the same behaviour? From the users' >>> perspective it looks like a bug in the downstream package, and I guess >>> many >>> people will not spot the obvious fix. >>> >>> Thanks, >>> >>> Malcolm >>> >>> PS Here is a self-contained example just using the core packages and no >>> external data: >>> >>> library(S4Vectors) >>> >>> setClass("CharacterVector", >>> representation(char_data = "character"), >>> contains="Vector" >>> ) >>> >>> setMethod(length, "CharacterVector", function(x) length(x@char_data)) >>> >>> char = new("CharacterVector", char_data=c("one", "two", "three")) >>> >>> mcols(char) = data.frame(number=1:3) # will fail >>> >>> mcols(char) = DataFrame(number=1:3) # fine >>> >>> library(GenomicRanges) >>> >>> gr = GRanges("chr", IRanges(1, 5)) >>> >>> mcols(gr) = data.frame(name="range1") >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel