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Question: Gviz BiomartGeneRegionTrack() error on filters use
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gravatar for iaingallagher
4 months ago by
iaingallagher0 wrote:

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           
ADD COMMENTlink modified 4 months ago • written 4 months ago by iaingallagher0

Ok, got it. Should be:

test <- BiomartGeneRegionTrack(biomart=mart, genome='hg19', name='ALDH6A1', gene='ENSG00000119711', filters=list(hgnc_symbol='ALDH6A1'))

From here: Gviz: BiomartGeneRegionTrack filters=??

best,

i

ADD REPLYlink written 4 months ago by iaingallagher0
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