Question: Gviz
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5.1 years ago by
Hi Jovana, UcscTracks uses the functionality provided by the rtracklayer package to communicate with UCSC, and only those tables that are supported by rtracklayer can be imported into Gviz. You can ask for the available tables using the tackNames function in combination with a session object: ses <- browserSession() genome(ses) <- "hg19" trackNames(ses) I will make this available as a more convenient function 'availableUcscTables' in Gviz with the next release. You can still use this data if you download it directly from the UCSC table browser to your computer and read in the data manually: aa <- read.delim("your.downloaded.file", foo <- DataTrack(chromosome=aa$chrom, start=aa$chromStart, end=aa$chromEnd, data=aa$score) This will work for any external data as long as it contains genomic coordinates and some data values. You may have to adapt the column mapping, of course. Florian -- From: Jovana Maksimovic <<>> Date: Thursday, November 15, 2012 5:34 AM To: NIBR <<>> Subject: Gviz Hi Florian, I’ve been using your Gviz package to make some wonderful figures using a combination of in house data and UCSC tracks. I’ve been running into an issue however with trying to add the UCSC Broad Histone data to some plots. I pretty much just copied the code for the GC percent track from your vignette, as I assumed it would be a similar type of plot. However, when I run the following code, I get the error message below: Gm12878H3k27ac <- UcscTrack(genome = gen, chromosome = paste("chr",chrom,sep=""), track = "Broad Histone", table = "wgEncodeBroadHistoneGm12878H3k27acStdPk", from = minbase, to = maxbase, trackType = "DataTrack", start = "chromStart", end = "chromEnd", data = "score", type = "hist", window = -1, windowSize = 1500, fill.histogram = "black", col.histogram = "black", ylim = c(30, 70), name = "Gm12878H3k27ac") Error in match.arg(track, sort(c(availTracks, names(availTracks)))) : 'arg' should be one of “5% Lowest S”, “acembly”, “AceView Genes”, “affyExonArray”, “Affy Exon Array”, “affyGnf1h”, “Affy GNF1H”, “Affy RNA Loc”, “affyU133”, “Affy U133”, “affyU133Plus2”, “Affy U133Plus2”, “affyU95”, “Affy U95”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “All SNPs(132)”, “All SNPs(135)”, “Alt Events”, “altSeqComposite9”, “Assembly”, “bacEndPairs”, “BAC End Pairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “Cand. Gene Flow”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “cgapSage”, “CGAP SAGE”, “chainSelf”, “Chromosome Band”, “Common SNPs(132)”, “Common SNPs(135)”, “cons46way”, “Conservation”, “consIndelsHgMmCanFam”, “Cons Indels MmCf”, “cosmic”, “COSMIC”, “cpgIslandExt”, “CpG Islands”, “CSHL Small RNA-seq”, “ctgPos”, “ctgPos2”, “cutters�� I’m guessing this might mean that I may not be able to use this track at all? Is there a particular reason for that? Also, is there some way to see all of the actually available tracks for the package. I understand that we can use the table browser at Ucsc, however, if there is a further limitation, it would be good to see the tracks that are actually accessible using Gviz. Apologies if I’ve overlooked something trivial, but any help you could provide in getting this to work (if at all possible) would be greatly appreciated. Thanks. Regards, Jovana > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 biomaRt_2.14.0 [3] Gviz_1.2.0 IlluminaHumanMethylation450k.db_1.4.7 [5] RSQLite_0.11.2 [7] DBI_0.2-5 AnnotationDbi_1.20.2 [9] limma_3.14.1 matrixStats_0.5.3 [11] gplots_2.11.0 MASS_7.3-22 [13] KernSmooth_2.23-8 caTools_1.13 [15] bitops_1.0-4.2 gdata_2.12.0 [17] gtools_2.7.0 RColorBrewer_1.0-5 [19] minfiData_0.3.1 IlluminaHumanMethylation450kmanifest_0.4.0 [21] minfi_1.4.0 Biostrings_2.26.2 [23] GenomicRanges_1.10.5 IRanges_1.16.4 [25] reshape_0.8.4 plyr_1.7.1 [27] lattice_0.20-10 Biobase_2.18.0 [29] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 annotate_1.36.0 beanplot_1.1 biovizBase_1.6.0 [5] bit_1.1-9 BSgenome_1.26.1 cluster_1.14.3 codetools_0.2-8 [9] colorspace_1.2-0 crlmm_1.16.4 dichromat_1.2-4 ellipse_0.3-7 [13] ff_2.2-10 foreach_1.4.0 genefilter_1.40.0 GenomicFeatures_1.10.0 [17] Hmisc_3.10-1 iterators_1.0.6 labeling_0.1 mclust_4.0 [21] multtest_2.14.0 munsell_0.4 mvtnorm_0.9-9993 nor1mix_1.1-3 [25] oligoClasses_1.20.0 parallel_2.15.0 preprocessCore_1.20.0 RCurl_1.95-3 [29] R.methodsS3_1.4.2 Rsamtools_1.10.2 rtracklayer_1.18.1 scales_0.2.2 [33] siggenes_1.32.0 splines_2.15.0 stats4_2.15.0 stringr_0.6.1 [37] survival_2.36-14 tools_2.15.0 XML_3.95-0.1 xtable_1.7-0 [41] zlibbioc_1.4.0 Jovana Maksimovic, PhD Postdoctoral Research Officer Quantitative Sciences Core, Bioinformatics Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 03 9936 6641<><http:""/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. 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ADD COMMENTlink written 5.1 years ago by florian.hahne@novartis.com1.5k
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