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iaingallagher
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@iaingallagher-13496
Last seen 6.7 years ago
Hi
I'm trying to build a track for only one gene. The Gviz documentation suggests that to do this with the BiomartGeneRegionTrack() function I have to pass in a biomart filter. Using the code below I get an error.
library(Gviz) library(biomaRt) mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") test <- BiomartGeneRegionTrack(biomart=mart, genome='hg19', name='ALDH6A1', symbol='ALDH6A1', filters=list('hgnc_symbol')) Error in getBM(as.vector(featureMap), filters = names(filterValues), values = filterValues, : Query ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method "isa" on unblessed reference at /nfs/public/release/ensweb/latest/live/mart/www_89/biomart-perl/lib/BioMart/Query.pm line 2117.
Any help would be appreciated.
Best,
Iain
sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods [10] base other attached packages: [1] biomaRt_2.32.1 Gviz_1.20.0 GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 [5] IRanges_2.10.2 S4Vectors_0.14.3 BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] Biobase_2.36.2 httr_1.2.1 bit64_0.9-7 [4] AnnotationHub_2.8.2 splines_3.4.0 shiny_1.0.3 [7] Formula_1.2-2 interactiveDisplayBase_1.14.0 latticeExtra_0.6-28 [10] blob_1.1.0 BSgenome_1.44.0 GenomeInfoDbData_0.99.0 [13] Rsamtools_1.28.0 yaml_2.1.14 RSQLite_2.0 [16] backports_1.1.0 lattice_0.20-35 biovizBase_1.24.0 [19] digest_0.6.12 RColorBrewer_1.1-2 XVector_0.16.0 [22] checkmate_1.8.3 colorspace_1.3-2 httpuv_1.3.5 [25] htmltools_0.3.6 Matrix_1.2-10 plyr_1.8.4 [28] XML_3.98-1.9 zlibbioc_1.22.0 xtable_1.8-2 [31] scales_0.4.1 BiocParallel_1.10.1 htmlTable_1.9 [34] tibble_1.3.3 AnnotationFilter_1.0.0 ggplot2_2.2.1 [37] SummarizedExperiment_1.6.3 GenomicFeatures_1.28.4 nnet_7.3-12 [40] lazyeval_0.2.0 mime_0.5 survival_2.41-3 [43] magrittr_1.5 memoise_1.1.0 foreign_0.8-69 [46] BiocInstaller_1.26.0 tools_3.4.0 data.table_1.10.4 [49] matrixStats_0.52.2 stringr_1.2.0 munsell_0.4.3 [52] cluster_2.0.6 DelayedArray_0.2.7 AnnotationDbi_1.38.1 [55] ensembldb_2.0.3 Biostrings_2.44.1 compiler_3.4.0 [58] rlang_0.1.1 RCurl_1.95-4.8 dichromat_2.0-0 [61] VariantAnnotation_1.22.3 htmlwidgets_0.9 bitops_1.0-6 [64] base64enc_0.1-3 gtable_0.2.0 curl_2.7 [67] DBI_0.7 R6_2.2.2 GenomicAlignments_1.12.1 [70] gridExtra_2.2.1 knitr_1.16 rtracklayer_1.36.4 [73] bit_1.1-12 Hmisc_4.0-3 ProtGenerics_1.8.0 [76] stringi_1.1.5 Rcpp_0.12.12 rpart_4.1-11 [79] acepack_1.4.1
Ok, got it. Should be:
From here: Gviz: BiomartGeneRegionTrack filters=??
best,
i