[Bioc-devel] Chromosome order in GRangesForUCSCGenome

[Bernat Gel]

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/>