[Bioc-devel] Chromosome order in GRangesForUCSCGenome

Bernat Gel bgel at igtp.cat
Tue Mar 14 12:21:15 CET 2017


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
bgel at igtp.cat <mailto:bgel at igtp.cat>
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 <bgel at igtp.cat 
> <mailto: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 <tel:%28%2B34%29%2093%20554%203068>
>     Fax: (+34) 93 497 8654 <tel:%28%2B34%29%2093%20497%208654>
>     08916 Badalona, Barcelona, Spain
>     bgel at igtp.cat <mailto:bgel at igtp.cat> <mailto:bgel at igtp.cat
>     <mailto:bgel at igtp.cat>>
>     www.germanstrias.org <http://www.germanstrias.org>
>     <http://www.germanstrias.org/>
>
>     <http://www.germanstrias.org/>
>
>
>
>
>
>
>
>     _______________________________________________
>     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
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