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