[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/>
>
>
>
>
>
>
>
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