Question: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
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gravatar for Christopher T Gregg
6.6 years ago by
Christopher T Gregg210 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 [[alternative HTML version deleted]]
biomart gviz • 1.4k views
ADD COMMENTlink modified 6.6 years ago by Robert Ivanek650 • written 6.6 years ago by Christopher T Gregg210
Answer: GViz trouble retreiving X chromosome data with BiomartGeneRegionTrack
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gravatar for Robert Ivanek
6.6 years ago by
Robert Ivanek650
Switzerland
Robert Ivanek650 wrote:
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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 6.6 years ago by Robert Ivanek650
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