Question: Error in Gviz BiomartGeneRegionTrack
gravatar for codezy
23 days ago by
codezy10 wrote:

Dear friends,

I would like to run the "BiomartGeneRegionTrack" in package Gviz to get the annotation file. But it seems I can not use the range function of it. Every time I get a start and end to "BiomartGeneRegionTrack" it will report an error. Moreover, "plotTracks" also shows nothing. The code is below:

> afrom <- 2960000
> ato <- 3160000
> bmt <- BiomartGeneRegionTrack(genome="hg19", chromosome="chr12", start=afrom, end=ato)
Warning message:
In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
>plotTracks(bmt, from=afrom, to=ato, chromosome="chr12")

Could anyone give me a tip about how to solve this problem? Thank you in advance.

ADD COMMENTlink written 23 days ago by codezy10

Hi codezy,

I use your codes and they work for me:


Can you provide the results from the following lines after you call bmt <- BiomartGeneRegionTrack(genome="hg19", ....):


My session info:

> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

[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      parallel  stats4    stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
[1] Gviz_1.26.5          GenomicRanges_1.34.0 GenomeInfoDb_1.18.2  IRanges_2.16.0      
[5] S4Vectors_0.20.1     BiocGenerics_0.28.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.42.0              httr_1.4.0                  bit64_0.9-7                
 [4] splines_3.5.3               Formula_1.2-3               assertthat_0.2.1           
 [7] latticeExtra_0.6-28         blob_1.1.1                  BSgenome_1.50.0            
[10] GenomeInfoDbData_1.2.0      Rsamtools_1.34.1            yaml_2.2.0                 
[13] progress_1.2.2              pillar_1.4.0                RSQLite_2.1.1              
[16] backports_1.1.4             lattice_0.20-38             biovizBase_1.30.1          
[19] glue_1.3.1                  digest_0.6.19               RColorBrewer_1.1-2         
[22] XVector_0.22.0              checkmate_1.9.3             colorspace_1.4-1           
[25] htmltools_0.3.6             Matrix_1.2-17               plyr_1.8.4                 
[28] XML_3.98-1.19               pkgconfig_2.0.2             biomaRt_2.38.0             
[31] zlibbioc_1.28.0             purrr_0.3.2                 scales_1.0.0               
[34] BiocParallel_1.16.6         tibble_2.1.1                htmlTable_1.13.1           
[37] AnnotationFilter_1.6.0      ggplot2_3.1.1               GenomicFeatures_1.34.8     
[40] SummarizedExperiment_1.12.0 nnet_7.3-12                 lazyeval_0.2.2             
[43] survival_2.44-1.1           magrittr_1.5                crayon_1.3.4               
[46] memoise_1.1.0               foreign_0.8-71              data.table_1.12.2          
[49] tools_3.5.3                 prettyunits_1.0.2           hms_0.4.2                  
[52] matrixStats_0.54.0          stringr_1.4.0               munsell_0.5.0              
[55] cluster_2.0.9               DelayedArray_0.8.0          ensembldb_2.6.8            
[58] AnnotationDbi_1.44.0        Biostrings_2.50.2           compiler_3.5.3             
[61] rlang_0.3.4                 RCurl_1.95-4.12             dichromat_2.0-0            
[64] rstudioapi_0.10             VariantAnnotation_1.28.13   htmlwidgets_1.3            
[67] bitops_1.0-6                base64enc_0.1-3             gtable_0.3.0               
[70] curl_3.3                    DBI_1.0.0                   R6_2.4.0                   
[73] GenomicAlignments_1.18.1    gridExtra_2.3               knitr_1.23                 
[76] dplyr_0.8.1                 rtracklayer_1.42.2          bit_1.1-14                 
[79] Hmisc_4.2-0                 ProtGenerics_1.14.0         stringi_1.4.3              
[82] Rcpp_1.0.1                  rpart_4.1-15                acepack_1.4.1              
[85] xfun_0.7                    tidyselect_0.2.5
ADD REPLYlink modified 23 days ago • written 23 days ago by SMK1.3k

Thank you @SMK. I reinstall my package and it works now.

ADD REPLYlink written 20 days ago by codezy10
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