Gviz::GeneRegionTrack error with standard TxDb: "adding seqlevels to a TxDb object is not supported"
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dbsgtk • 0
@dbsgtk-7331
Last seen 12 months ago
Singapore

I've started getting an unexpected result that prevents me from displaying a GeneRegionTrack with a standard genome imports. Setting up as follows:

GRCh38 <- makeTxDbFromEnsembl(tx_attrib="gencode_basic")
goi <- "ENSG00000147457"
gr <- genes(GRCh38)[goi]
gr

Gives me the expected GRange.

GRanges object with 1 range and 1 metadata column:
       seqnames                     ranges   strand   |         gene_id
          <Rle>                  <IRanges>    <Rle>   |     <character>
ENSG00000147457     chr8 23243637-23262000        +   | ENSG00000147457

seqinfo: 25 sequences (1 circular) from an unspecified genome; no seqlengths

But when using that range to construct input into a GeneRegion track,

GeneRegionTrack(GRCh38,chromosome = as.character(chrom(gr)),
                from=start(gr),
                to=end(gr))

I'm getting an error:

Error in `seqlevels<-`(`*tmp*`, pruning.mode = "coarse", value = "chr8") : 
  adding seqlevels to a TxDb object is not supported

I've tried changing versions of both Gviz and GenomeInfoDb, but to no avail

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3;  LAPACK version 3.10.0

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=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Singapore
tzcode source: system (glibc)

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Gviz_1.46.0                 DESeq2_1.42.0               SummarizedExperiment_1.32.0
 [4] MatrixGenerics_1.14.0       matrixStats_1.0.0           GEOquery_2.70.0            
 [7] rtracklayer_1.62.0          lubridate_1.9.3             forcats_1.0.0              
[10] stringr_1.5.0               dplyr_1.1.3                 purrr_1.0.2                
[13] readr_2.1.4                 tidyr_1.3.0                 tibble_3.2.1               
[16] ggplot2_3.4.4               tidyverse_2.0.0             here_1.0.1                 
[19] ensembldb_2.26.0            AnnotationFilter_1.26.0     GenomicFeatures_1.54.1     
[22] AnnotationDbi_1.64.0        Biobase_2.62.0              GenomicRanges_1.54.1       
[25] GenomeInfoDb_1.38.0         IRanges_2.36.0              S4Vectors_0.40.1           
[28] AnnotationHub_3.10.0        BiocFileCache_2.10.1        dbplyr_2.4.0               
[31] BiocGenerics_0.48.0         devtools_2.4.5              usethis_2.2.2              

loaded via a namespace (and not attached):
  [1] later_1.3.1                   BiocIO_1.12.0                
  [3] bitops_1.0-7                  filelock_1.0.2               
  [5] janitor_2.2.0                 XML_3.99-0.14                
  [7] rpart_4.1.21                  lifecycle_1.0.3              
  [9] rprojroot_2.0.3               vroom_1.6.4                  
 [11] processx_3.8.2                lattice_0.22-5               
 [13] backports_1.4.1               magrittr_2.0.3               
 [15] limma_3.58.1                  Hmisc_5.1-1                  
 [17] rmarkdown_2.25                yaml_2.3.7                   
 [19] remotes_2.4.2.1               httpuv_1.6.12                
 [21] sessioninfo_1.2.2             pkgbuild_1.4.2               
 [23] DBI_1.1.3                     RColorBrewer_1.1-3           
 [25] abind_1.4-5                   pkgload_1.3.3                
 [27] zlibbioc_1.48.0               biovizBase_1.50.0            
 [29] RCurl_1.98-1.12               nnet_7.3-19                  
 [31] VariantAnnotation_1.48.0      rappdirs_0.3.3               
 [33] GenomeInfoDbData_1.2.11       codetools_0.2-19             
 [35] DelayedArray_0.28.0           xml2_1.3.5                   
 [37] tidyselect_1.2.0              base64enc_0.1-3              
 [39] GenomicAlignments_1.38.0      ellipsis_0.3.2               
 [41] Formula_1.2-5                 tools_4.3.1                  
 [43] progress_1.2.2                Rcpp_1.0.11                  
 [45] glue_1.6.2                    gridExtra_2.3                
 [47] SparseArray_1.2.0             xfun_0.41                    
 [49] withr_2.5.2                   BiocManager_1.30.22          
 [51] fastmap_1.1.1                 latticeExtra_0.6-30          
 [53] fansi_1.0.5                   callr_3.7.3                  
 [55] digest_0.6.33                 timechange_0.2.0             
 [57] R6_2.5.1                      mime_0.12                    
 [59] colorspace_2.1-0              jpeg_0.1-10                  
 [61] dichromat_2.0-0.1             biomaRt_2.58.0               
 [63] RSQLite_2.3.2                 utf8_1.2.4                   
 [65] generics_0.1.3                data.table_1.14.8            
 [67] prettyunits_1.2.0             httr_1.4.7                   
 [69] htmlwidgets_1.6.2             S4Arrays_1.2.0               
 [71] pkgconfig_2.0.3               gtable_0.3.4                 
 [73] blob_1.2.4                    XVector_0.42.0               
 [75] htmltools_0.5.6.1             profvis_0.3.8                
 [77] ProtGenerics_1.34.0           scales_1.2.1                 
 [79] RMariaDB_1.3.1                png_0.1-8                    
 [81] snakecase_0.11.1              knitr_1.45                   
 [83] rstudioapi_0.15.0             tzdb_0.4.0                   
 [85] rjson_0.2.21                  checkmate_2.3.0              
 [87] curl_5.1.0                    cachem_1.0.8                 
 [89] BiocVersion_3.18.0            parallel_4.3.1               
 [91] miniUI_0.1.1.1                foreign_0.8-85               
 [93] desc_1.4.2                    restfulr_0.0.15              
 [95] pillar_1.9.0                  vctrs_0.6.4                  
 [97] urlchecker_1.0.1              promises_1.2.1               
 [99] xtable_1.8-4                  cluster_2.1.4                
[101] htmlTable_2.4.2               evaluate_0.23                
[103] cli_3.6.1                     locfit_1.5-9.8               
[105] compiler_4.3.1                Rsamtools_2.18.0             
[107] rlang_1.1.1                   crayon_1.5.2                 
[109] interp_1.1-4                  ps_1.7.5                     
[111] fs_1.6.3                      stringi_1.7.12               
[113] deldir_1.0-9                  BiocParallel_1.36.0          
[115] munsell_0.5.0                 Biostrings_2.70.1            
[117] lazyeval_0.2.2                Matrix_1.6-1.1               
[119] BSgenome_1.70.0               hms_1.1.3                    
[121] bit64_4.0.5                   KEGGREST_1.42.0              
[123] statmod_1.5.0                 shiny_1.7.5.1                
[125] interactiveDisplayBase_1.40.0 memoise_2.0.1                
[127] bit_4.0.5
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