Re: [Bioc-devel] Chromosome order in GRangesForUCSCGenome

Tue, 14 Mar 2017 04:22:41 -0700 

Great, thanks

*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
[email protected] <mailto:[email protected]>
www.germanstrias.org <http://www.germanstrias.org/>

<http://www.germanstrias.org/>







El 03/13/2017 a las 01:57 PM, Michael Lawrence escribió:
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 <[email protected] <mailto:[email protected]>> 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 <tel:%28%2B34%29%2093%20554%203068>
    Fax: (+34) 93 497 8654 <tel:%28%2B34%29%2093%20497%208654>
    08916 Badalona, Barcelona, Spain
    [email protected] <mailto:[email protected]> <mailto:[email protected]
    <mailto:[email protected]>>
    www.germanstrias.org <http://www.germanstrias.org>
    <http://www.germanstrias.org/>

    <http://www.germanstrias.org/>







    _______________________________________________
    [email protected] <mailto:[email protected]> mailing
    list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel
    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>




_______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Reply via email to