[Bioc-devel] Chromosome order in GRangesForUCSCGenome

[Michael Lawrence]

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 <bgel at 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, Camí de les Escoles s/n
> 08916 Badalona, Barcelona, Spain
>
> Tel: (+34) 93 554 3068
> Fax: (+34) 93 497 8654
> 08916 Badalona, Barcelona, Spain
> bgel at igtp.cat <mailto:bgel at igtp.cat>
> www.germanstrias.org <http://www.germanstrias.org/>
>
> <http://www.germanstrias.org/>
>
>
>
>
>
>
>
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