Question: Gviz : UcscTrack ..
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gravatar for Tim Smith
7.2 years ago by
Tim Smith1.1k
Tim Smith1.1k wrote:
Hi, I was trying the code in the reference manual to get the GC content but it's giving errors. All the parameters appear to be correct (I checked with UCSC) - here is the code, as given in the manual: ############### from <- 65921878 to <- 65980988 gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX",    track = "GC Percent", table = "gc5Base", from = from,          to = to, trackType = "DataTrack", start = "start", end = "end", data = "score",          type = "hist", window = -1, windowSize = 1500, fill.histogram = "black",          "darkblue",col.histogram = "black", ylim = c(30, 70), name = "GC Percent") ############## The errors that I get: Error in UcscTrack(genome = "mm9", chromosome = "chrX", track = "GC Percent",  :   Error fetching data from UCSC In addition: Warning message: In UcscTrack(genome = "mm9", chromosome = "chrX", track = "GC Percent",  :   Error in try(track(query), silent = TRUE) :   could not find function "track" thanks!! My sessioninfo: > sessionInfo() R version 2.15.0 (2012-03-30) 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 [7] methods   base other attached packages:  [1] IRanges_1.14.2        Gviz_1.0.1  [3] xtable_1.7-0          GenomeGraphs_1.16.0  [5] quantsmooth_1.22.0    lodplot_1.1  [7] quantreg_4.79         SparseM_0.96  [9] seqLogo_1.18.0        hash_2.1.0.2 [11] impute_1.30.0         ggdendro_0.1-05 [13] ggplot2_0.9.0         XML_3.9-4 [15] hgu133a.db_2.7.1      affy_1.34.0 [17] genefilter_1.38.0     biomaRt_2.12.0 [19] org.Hs.eg.db_2.7.1    GOstats_2.22.0 [21] graph_1.34.0          Category_2.22.0 [23] GO.db_2.7.1           RSQLite_0.11.1 [25] DBI_0.2-5             AnnotationDbi_1.18.0 [27] Biobase_2.16.0        BiocGenerics_0.2.0 [29] fExtremes_2100.77     fTrading_2100.76 [31] fGarch_2110.80        fBasics_2160.81 [33] MASS_7.3-18           timeSeries_2160.94 [35] timeDate_2160.95      lattice_0.20-6 [37] gap_1.1-6             plotrix_3.4 [39] som_0.3-5             gplots_2.10.1 [41] KernSmooth_2.23-7     caTools_1.12 [43] bitops_1.0-4.1        gdata_2.8.2 [45] pvclust_1.2-2         reshape_0.8.4 [47] plyr_1.7.1            zoo_1.7-7 [49] data.table_1.8.0      foreach_1.4.0 [51] foreign_0.8-49        languageR_1.4 [53] preprocessCore_1.18.0 gtools_2.6.2 [55] BiocInstaller_1.4.7 loaded via a namespace (and not attached):  [1] affyio_1.24.0       annotate_1.34.0     Biostrings_2.24.1  [4] BSgenome_1.24.0     codetools_0.2-8     colorspace_1.1-1  [7] dichromat_1.2-4     digest_0.5.2        GenomicRanges_1.8.5 [10] GSEABase_1.18.0     iterators_1.0.6     memoise_0.1 [13] munsell_0.3         proto_0.3-9.2       RBGL_1.32.0 [16] RColorBrewer_1.0-5  RCurl_1.91-1        reshape2_1.2.1 [19] Rsamtools_1.8.4     rtracklayer_1.16.1  scales_0.2.0 [22] splines_2.15.0      stabledist_0.6-3    stats4_2.15.0 [25] stringr_0.6         survival_2.36-14    tools_2.15.0 [28] zlibbioc_1.2.0 > [[alternative HTML version deleted]]
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ADD COMMENTlink written 7.2 years ago by Tim Smith1.1k
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