seqlevelsStyle() not working
2
@kai
Last seen 3 days 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Seems that the URL is no longer valid, and has been replaced with: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
• 360 views
@kentriemondy-14219
Last seen 16 hours 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 2 days 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!