seqlevelsStyle() not working
2
@kai
Last seen 3 months ago
Worcester
I got the following error when invoking seqlevelsStyle()
:
seqlevelsStyle(annoData) <- "UCSC"
Error in download.file(url, destfile, quiet = TRUE) :
cannot open URL 'https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz'
Seems that the URL is no longer valid, and has been replaced with:
https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
The following link seems to work as well:
https://hgdownload2.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
Any input on how to solve this and which link should be used for downloading?
ensembldb
genomei
GenomeInfoDb
• 699 views
@kentriemondy-14219
Last seen 6 weeks ago
Denver, University of Colorado Anschutz…
An update to the GenomeDbInfo
package was pushed to Bioconductor 3.18 recently that should fix this and will be available in a day or two. In the meantime you can change the domain used by seqlevelsStyle()
by setting this option in your session:
options(UCSC.goldenPath.url="https://hgdownload.soe.ucsc.edu/goldenPath")
@james-w-macdonald-5106
Last seen 1 day ago
United States
Do you need to update your versions of R/Bioconductor?
> gr <- GRanges("1:100-1000")
> seqlevelsStyle(gr) <- "UCSC"
> gr
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 100-1000 *
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics
[4] grDevices utils datasets
[7] methods base
other attached packages:
[1] GenomicFeatures_1.54.1
[2] AnnotationDbi_1.64.1
[3] Biobase_2.62.0
[4] GenomicRanges_1.54.1
[5] GenomeInfoDb_1.38.5
[6] IRanges_2.36.0
[7] S4Vectors_0.40.2
[8] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] KEGGREST_1.42.0
[2] SummarizedExperiment_1.32.0
[3] rjson_0.2.21
[4] lattice_0.22-5
[5] vctrs_0.6.5
[6] tools_4.3.1
[7] bitops_1.0-7
[8] generics_0.1.3
[9] curl_5.2.0
[10] parallel_4.3.1
[11] tibble_3.2.1
[12] fansi_1.0.6
[13] RSQLite_2.3.5
[14] blob_1.2.4
[15] pkgconfig_2.0.3
[16] Matrix_1.6-5
[17] dbplyr_2.4.0
[18] lifecycle_1.0.4
[19] GenomeInfoDbData_1.2.11
[20] compiler_4.3.1
[21] stringr_1.5.1
[22] Rsamtools_2.18.0
[23] Biostrings_2.70.2
[24] progress_1.2.3
[25] codetools_0.2-19
[26] RCurl_1.98-1.14
[27] yaml_2.3.8
[28] pillar_1.9.0
[29] crayon_1.5.2
[30] BiocParallel_1.36.0
[31] DelayedArray_0.28.0
[32] cachem_1.0.8
[33] abind_1.4-5
[34] tidyselect_1.2.0
[35] digest_0.6.34
[36] stringi_1.8.3
[37] dplyr_1.1.4
[38] restfulr_0.0.15
[39] grid_4.3.1
[40] biomaRt_2.58.1
[41] fastmap_1.1.1
[42] SparseArray_1.2.3
[43] cli_3.6.2
[44] magrittr_2.0.3
[45] S4Arrays_1.2.0
[46] XML_3.99-0.16.1
[47] utf8_1.2.4
[48] prettyunits_1.2.0
[49] filelock_1.0.3
[50] rappdirs_0.3.3
[51] bit64_4.0.5
[52] XVector_0.42.0
[53] httr_1.4.7
[54] matrixStats_1.2.0
[55] bit_4.0.5
[56] png_0.1-8
[57] hms_1.1.3
[58] memoise_2.0.1
[59] BiocIO_1.12.0
[60] BiocFileCache_2.10.1
[61] rtracklayer_1.62.0
[62] rlang_1.1.3
[63] glue_1.7.0
[64] DBI_1.2.1
[65] xml2_1.3.6
[66] R6_2.5.1
[67] MatrixGenerics_1.14.0
[68] GenomicAlignments_1.38.2
[69] zlibbioc_1.48.0
>
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Ty, this works for me!