Good to hear, thanks for the update, it makes best sense to me, and is most consistent with names elsewhere in R.
~Malcolm > -----Original Message----- > From: Hervé Pagès [mailto:hpa...@fhcrc.org] > Sent: Wednesday, August 03, 2011 2:47 PM > To: Cook, Malcolm > Cc: 'bioc-sig-sequencing@r-project.org' > Subject: Re: [Bioc-sig-seq] GRangesList with duplicate names - > WORKAROUND > > Hi Malcolm, > > The requirement that names of a GRangesList must be unique has actually > been dropped in BioC 2.9 (current devel): > > > library(GenomicRanges) > > grl <- GRangesList(a=GRanges(), a=GRanges()) > > validObject(grl) > [1] TRUE > > Note that before BioC 2.9 this requirement was not only for GRangesList > but also for GRanges objects. In BioC 2.9, this requirement has been > dropped for both containers: > > > gr <- GRanges(c("chr1", "chr1"), IRanges(1:2, 4:5, names=c("a", "a"))) > > validObject(gr) > [1] TRUE > > Cheers, > H. > > > sessionInfo() > R Under development (unstable) (2011-07-31 r56578) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 > [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures_1.5.16 GenomicRanges_1.5.21 IRanges_1.11.17 > > loaded via a namespace (and not attached): > [1] Biobase_2.13.7 biomaRt_2.9.2 Biostrings_2.21.7 > [4] BSgenome_1.21.3 DBI_0.2-5 RCurl_1.6-6 > [7] RSQLite_0.9-4 rtracklayer_1.13.10 XML_3.4-0 > [10] zlibbioc_0.1.7 > > > On 11-08-03 09:23 AM, Cook, Malcolm wrote: > > Hi, > > > > re: https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011- > February/001867.html > > > > It appears that the requirement that names of a GRangesList must be > unique has won the day. > > > > I'm not sure I agree with this result, as there are many operations that are > optimized for GRangesList that have use cases that do not depend upon such > uniqueness. > > > > However, I find that such operations can proceed after setting the names > to NULL,, as is demonstrated in the R session following my signature, in which > I am creating a GRanges list with entirely duplicate (unnamed) elements. > > > > I hope this workaround proves useful to others... > > > > Malcolm Cook > > Computational Biology - Stowers Institute for Medical Research > > > > > > > > Example: > > > >> > grl=GRangesList(a=GRanges(c(10,20,30),c(15,25,35)),b=GRanges(c(100,200,3 > 00),c(150,250,350))) > >> grl > > GRangesList of length 2 > > $a > > GRanges with 3 ranges and 0 elementMetadata values > > seqnames ranges strand | > > <Rle> <IRanges> <Rle> | > > [1] 10 [15, 15] * | > > [2] 20 [25, 25] * | > > [3] 30 [35, 35] * | > > > > $b > > GRanges with 3 ranges and 0 elementMetadata values > > seqnames ranges strand | > > <Rle> <IRanges> <Rle> | > > [1] 100 [150, 150] * | > > [2] 200 [250, 250] * | > > [3] 300 [350, 350] * | > > > > > > seqlengths > > 10 20 30 100 200 300 > > NA NA NA NA NA NA > >> grl[rep(1,2)] > > Error in `rownames<-`(`*tmp*`, value = c("a", "a")) : > > duplicate rownames not allowed > >> names(grl)=NULL > >> grl[rep(1,2)] > > GRangesList of length 2 > > [[1]] > > GRanges with 3 ranges and 0 elementMetadata values > > seqnames ranges strand | > > <Rle> <IRanges> <Rle> | > > [1] 10 [15, 15] * | > > [2] 20 [25, 25] * | > > [3] 30 [35, 35] * | > > > > [[2]] > > GRanges with 3 ranges and 0 elementMetadata values > > seqnames ranges strand | > > <Rle> <IRanges> <Rle> | > > [1] 10 [15, 15] * | > > [2] 20 [25, 25] * | > > [3] 30 [35, 35] * | > > > > > > seqlengths > > 10 20 30 100 200 300 > > NA NA NA NA NA NA > >> > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > Bioc-sig-sequencing@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > -- > 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...@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing