Right, match.fun() needs to be within the initial endoapply, not later. Isn't the convention though to use `obeyQname<-` in this case? Or should there be a convention?
On Wed, Nov 20, 2013 at 5:18 PM, Martin Morgan <mtmor...@fhcrc.org> wrote: > After this > > library(RNAseqData.HNRNPC.bam.chr14) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES > exByGn <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene") > > Rsamtools is loaded but not attached; it's > summarizeOverlaps,GRanges,character-method > is available (maybe it shouldn't be, but that's a different question). > Invoking > > summarizeOverlaps(exByGn, fls) > > results in > > > summarizeOverlaps(exByGn, fls) > Error in get(as.character(FUN), mode = "function", envir = envir) : > object 'obeyQname<-' of mode 'function' was not found > > with > > > traceback() > 14: get(as.character(FUN), mode = "function", envir = envir) > 13: match.fun(FUN) > 12: lapply(as.list(X), FUN = FUN, ...) > 11: lapply(as.list(X), FUN = FUN, ...) > 10: lapply(X, FUN = FUN, ...) > 9: lapply(X, FUN = FUN, ...) > 8: endoapply(object, "obeyQname<-", value = value) > 7: endoapply(object, "obeyQname<-", value = value) > 6: `obeyQname<-`(`*tmp*`, value = FALSE) > 5: `obeyQname<-`(`*tmp*`, value = FALSE) > 4: BamFileList(reads, yieldSize = yieldSize, obeyQname = FALSE, > asMates = !singleEnd) > 3: .local(features, reads, mode, ignore.strand, ...) > 2: summarizeOverlaps(exByGn, fls) > 1: summarizeOverlaps(exByGn, fls) > > and the parent.frame() of the environment (where the search at line 14 > starts) is IRanges, but should be Rsamtools (where endoapply was invoked). > > Martin > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
