txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
1
0
Entering edit mode
@3aae7d29
Last seen 3 days ago
France

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

```

TxDb.Mmusculus.UCSC.mm10.ensGene TxDb karyoploteR • 212 views
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0
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@james-w-macdonald-5106
Last seen 4 days ago
United States

The default for plotKaryotype is to use hg19.

0
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thanks for the reply. plotKaryotype works fine with other mm10 regions, this specific part of X chromosome seems to be the issue.

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0
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James is right, it is using "hg19" if no genome is specified. The other regions probably worked because they are also correct on the human genome. You should simply specify the genome with

region <- toGRanges("chrX:167,150,253-167,426,555")
kp <- plotKaryotype(genoem="mm10", zoom =region)

and that should do the trick.

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1
Entering edit mode

That indeed worked, thanks a lot for the help (and for karyoploteR)

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