[BioC] GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack

[Robert Ivanek]

Dear Chris,

You have to run the code "options(ucscChromosomeNames=FALSE)" before
calling the function BiomartGeneRegionTrack. Gviz currently assumes
chromosome names in UCSC style like "chr1", "chrX" etc. following should
work for you.

library("Gviz")
library("GenomicRanges")
library("biomaRt")
library("BiocGenerics")
ensembl67 <- useMart(host='may2012.archive.ensembl.org',
biomart='ENSEMBL_MART_ENSEMBL') #uses ensemble67 build
("may2012.archive.ensembl.org")
ensembl67 <- useDataset("mmusculus_gene_ensembl", mart=ensembl67)

options(ucscChromosomeNames=FALSE)
biomTrack <- BiomartGeneRegionTrack(genome = "mm9", biomart = ensembl67,
chromosome = "X", start = 166123129, end = 166443668, stacking="squish",
showId = TRUE, name= "geneName")

Best
Robert

On 12/04/13 18:49, chris_utah wrote:
> Hi,
> 
> I am encountering an error when attempting to retrieve data from the X chromosome using GViz.  The error is unclear to me and I would greatly appreciate some help.
> 
> The code and error and sessionInfo() are below.  Please note that I have tried the code with and without ucscChromosomeNames=FALSE.
> 
> Thank you very much.
> 
> best wishes,
> Chris
> 
> CODE:
> ##################################################
> library("Gviz")
> library("GenomicRanges")
> library("biomaRt")
> library("BiocGenerics")
> ensembl67 =useMart(host='may2012.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL') #uses ensemble67 build ("may2012.archive.ensembl.org")
> ensembl67 = useDataset("mmusculus_gene_ensembl", mart=ensembl67)
> biomTrack <- BiomartGeneRegionTrack(genome = "mm9", biomart = ensembl67, chromosome = "X", start = 166123129, end = 166443668, stacking="squish", showId = TRUE, name= geneName, ucscChromosomeNames=FALSE)
> 
> 
> ERROR:
>> 	biomTrack <- BiomartGeneRegionTrack(genome = "mm9", biomart = ensembl67, chromosome = "X", start = startGene, end = endGene, stacking="squish", showId = TRUE, name= geneName, ucscChromosomeNames=FALSE)
> Error in FUN("X"[[1L]], ...) : Invalid chromosome identifier 'x'
> Please consider setting options(ucscChromosomeNames=FALSE) to allow for arbitrary chromosome identifiers.
> 
> 
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] edgeR_3.0.8          limma_3.14.4         biomaRt_2.14.0       GenomicRanges_1.10.7 IRanges_1.16.6       BiocGenerics_0.4.0  
> [7] Gviz_1.2.1          
> 
> loaded via a namespace (and not attached):
>  [1] annotate_1.36.0        AnnotationDbi_1.20.6   Biobase_2.18.0         Biostrings_2.26.3      biovizBase_1.6.2       bitops_1.0-4.2        
>  [7] BSgenome_1.26.1        cluster_1.14.3         colorspace_1.2-1       DBI_0.2-5              DESeq_1.10.1           dichromat_2.0-0       
> [13] genefilter_1.40.0      geneplotter_1.36.0     GenomicFeatures_1.10.2 Hmisc_3.10-1           labeling_0.1           lattice_0.20-13       
> [19] munsell_0.4            parallel_2.15.2        plyr_1.8               RColorBrewer_1.0-5     RCurl_1.95-4.1         Rsamtools_1.10.2      
> [25] RSQLite_0.11.2         rtracklayer_1.18.2     scales_0.2.3           splines_2.15.2         stats4_2.15.2          stringr_0.6.2         
> [31] survival_2.37-4        tools_2.15.2           XML_3.95-0.2           xtable_1.7-1           zlibbioc_1.4.0        
> 
> 
> 
> Christopher Gregg, PhD.
> New York Stem Cell Foundation-Robertson Investigator
> Assistant Professor, Neurobiology and Anatomy
> Adjunct Assistant Professor, Human Genetics
> 323 Wintrobe Bldg 530
> University of Utah, School of Medicine
> 20 North 1900 East
> Salt Lake City, Utah 84132-3401
> 
> phone: (801) 581-8212
> fax: (801) 585-9736
> ------------------------------------
> Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html
> 
> 
> 
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> 
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