Looks like UCSC has started sorting the chromosomes by size. I made 1.35.9 use sortSeqlevels() to normalize the order of them.
On Mon, Mar 13, 2017 at 3:05 AM, Bernat Gel <b...@igtp.cat> wrote: > I'm downloading genome information from UCSC using the > GRangesForUCSCGenome from rtracklayer and it seems that the chromosome > order is incorrect (or at least non-canonical). > > > seqlevels(GRangesForUCSCGenome(genome="hg19")) > > [1] "chr1" "chr2" "chr3" "chr4" "chr5" > [6] "chr6" "chr7" "chrX" "chr8" "chr9" > [11] "chr10" "chr11" "chr12" "chr13" > "chr14" > [16] "chr15" "chr16" "chr17" "chr18" > "chr20" > [21] "chrY" "chr19" "chr22" "chr21" > "chr6_ssto_hap7" > [26] ... > > With chrX before chr8 and Y before chr19. > > And the same happens with SeqinfoForUCSCGenome(genome="hg19") > > I know I could reorder them manually, but I'm downloading this from > various genomes to cache them in a package (karyoploteR) and I'd rather not > rely on manual sorting for that. > > I'm quite sure it used to return them in the canonical order. Is there > anything I'm missing or is it a bug somewhere? > > > Thanks a lot > > Bernat > > > > > sessionInfo() > R Under development (unstable) (2016-11-07 r71637) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Debian GNU/Linux 8 (jessie) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C > LC_COLLATE=en_US.utf8 LC_MONETARY=en_US.utf8 > [6] LC_MESSAGES=en_US.utf8 LC_PAPER=es_ES.UTF-8 LC_NAME=C > LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] testthat_1.0.2 karyoploteR_0.99.8 biovizBase_1.23.2 > regioneR_1.7.1 BSgenome_1.43.2 rtracklayer_1.35.1 > [7] Biostrings_2.43.2 XVector_0.15.0 GenomicRanges_1.27.18 > GenomeInfoDb_1.11.6 IRanges_2.9.14 S4Vectors_0.13.5 > [13] BiocGenerics_0.21.1 memoise_1.0.0 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.8 lattice_0.20-34 Rsamtools_1.27.11 > assertthat_0.1 > [5] digest_0.6.11 mime_0.5 R6_2.2.0 > plyr_1.8.4 > [9] backports_1.0.4 acepack_1.4.1 RSQLite_1.1-2 > httr_1.2.1 > [13] ggplot2_2.2.1 BiocInstaller_1.25.3 zlibbioc_1.21.0 > GenomicFeatures_1.27.6 > [17] lazyeval_0.2.0 data.table_1.10.0 rpart_4.1-10 > Matrix_1.2-7.1 > [21] checkmate_1.8.2 splines_3.4.0 BiocParallel_1.9.4 > AnnotationHub_2.7.9 > [25] stringr_1.1.0 foreign_0.8-67 ProtGenerics_1.7.0 > RCurl_1.95-4.8 > [29] biomaRt_2.31.3 munsell_0.4.3 shiny_0.14.2 > httpuv_1.3.3 > [33] base64enc_0.1-3 htmltools_0.3.5 nnet_7.3-12 > SummarizedExperiment_1.5.3 > [37] tibble_1.2 gridExtra_2.2.1 htmlTable_1.8 > interactiveDisplayBase_1.13.0 > [41] Hmisc_4.0-2 XML_3.98-1.5 crayon_1.3.2 > GenomicAlignments_1.11.6 > [45] bitops_1.0-6 grid_3.4.0 xtable_1.8-2 > gtable_0.2.0 > [49] DBI_0.5-1 magrittr_1.5 scales_0.4.1 > stringi_1.1.2 > [53] latticeExtra_0.6-28 Formula_1.2-1 RColorBrewer_1.1-2 > ensembldb_1.99.10 > [57] tools_3.4.0 dichromat_2.0-0 Biobase_2.35.0 > survival_2.40-1 > [61] yaml_2.1.14 AnnotationDbi_1.37.0 colorspace_1.3-2 > cluster_2.0.5 > [65] VariantAnnotation_1.21.14 knitr_1.15.1 > > > -- > > *Bernat Gel Moreno* > Bioinformatician > > Hereditary Cancer Program > Program of Predictive and Personalized Medicine of Cancer (PMPPC) > Germans Trias i Pujol Research Institute (IGTP) > > Campus Can Ruti > Carretera de Can Ruti, Camà de les Escoles s/n > 08916 Badalona, Barcelona, Spain > > Tel: (+34) 93 554 3068 > Fax: (+34) 93 497 8654 > 08916 Badalona, Barcelona, Spain > b...@igtp.cat <mailto:b...@igtp.cat> > www.germanstrias.org <http://www.germanstrias.org/> > > <http://www.germanstrias.org/> > > > > > > > > _______________________________________________ > 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