Hello, I'm trying to plot genomics data in the vicinity of the Tlr7/8 genes on the X chromosome using karyoploteR and there seems to be an issue with the coordinates in that region:
region <- toGRanges("chrX:167,150,253-167,426,555")
kp <- plotKaryotype(zoom =region)
gives me the following error: Error in plotKaryotype(zoom = region) : You are trying to set the zoom to a region not part of the current genome.
That region is indeed in the mm10 reference and
seqinfo(TxDb.Mmusculus.UCSC.mm10.knownGene)
shows a seqlength of 171031299 for chrX so the chromosome end should be roughtly 3.6Mb away from my ROI. I was thus wondering whether there could be an error in this specific TxDb version.
Thanks in advance
sessionInfo( ) R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS 15.1.1
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Paris tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] karyoploteR_1.30.0 regioneR_1.36.0
[3] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 GenomicFeatures_1.56.0
[5] AnnotationDbi_1.66.0 Biobase_2.64.0
[7] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1
[9] IRanges_2.38.1 S4Vectors_0.42.1
[11] BiocGenerics_0.50.0 BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-9 gridExtra_2.3 rlang_1.1.4
[5] magrittr_2.0.3 biovizBase_1.52.0 matrixStats_1.4.1 compiler_4.4.1
[9] RSQLite_2.3.8 png_0.1-8 vctrs_0.6.5 ProtGenerics_1.36.0
[13] stringr_1.5.1 pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0
[17] backports_1.5.0 XVector_0.44.0 utf8_1.2.4 Rsamtools_2.20.0
[21] rmarkdown_2.29 UCSC.utils_1.0.0 bit_4.5.0 xfun_0.49
[25] zlibbioc_1.50.0 cachem_1.1.0 jsonlite_1.8.9 blob_1.2.4
[29] DelayedArray_0.30.1 BiocParallel_1.38.0 parallel_4.4.1 cluster_2.1.6
[33] R6_2.5.1 VariantAnnotation_1.50.0 stringi_1.8.4 RColorBrewer_1.1-3
[37] bezier_1.1.2 rtracklayer_1.64.0 rpart_4.1.23 Rcpp_1.0.13-1
[41] SummarizedExperiment_1.34.0 knitr_1.49 base64enc_0.1-3 Matrix_1.7-1
[45] nnet_7.3-19 tidyselect_1.2.1 dichromat_2.0-0.1 rstudioapi_0.17.1
[49] abind_1.4-8 yaml_2.3.10 codetools_0.2-20 curl_6.0.1
[53] lattice_0.22-6 tibble_3.2.1 KEGGREST_1.44.1 evaluate_1.0.1
[57] foreign_0.8-87 Biostrings_2.72.1 pillar_1.9.0 MatrixGenerics_1.16.0
[61] checkmate_2.3.2 generics_0.1.3 RCurl_1.98-1.16 ensembldb_2.28.1
[65] ggplot2_3.5.1 munsell_0.5.1 scales_1.3.0 glue_1.8.0
[69] lazyeval_0.2.2 Hmisc_5.2-0 tools_4.4.1 BiocIO_1.14.0
[73] data.table_1.16.2 BSgenome_1.72.0 GenomicAlignments_1.40.0 XML_3.99-0.17
[77] grid_4.4.1 colorspace_2.1-1 GenomeInfoDbData_1.2.12 htmlTable_2.4.3
[81] restfulr_0.0.15 Formula_1.2-5 cli_3.6.3 fansi_1.0.6
[85] S4Arrays_1.4.1 dplyr_1.1.4 AnnotationFilter_1.28.0 gtable_0.3.6
[89] digest_0.6.37 SparseArray_1.4.8 rjson_0.2.23 htmlwidgets_1.6.4
[93] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7
[97] bit64_4.5.2 bamsignals_1.36.0
```
