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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