Open prc992 opened 7 months ago
maximilianh
commented
7 months ago The only context that I can add is that ncbiRefSeq is a table, and refSeqComposite is its parent container track, but the container does not have a table or data, it's just an empty shell for the UI. Why rtracklayer thinks that refSeqComposite is relevant here is a mystery to me, but I'm not an rtracklayer expert.
sanchit-saini
commented
7 months ago I tested it and could not replicate it. Can you make sure all packages are updated to the latest Bioconductor 3.18 (release)? By running following code and test it again whether it is fixed or not:
BiocManager::install(version = "3.18")library(Gviz)
ucscGenes <- UcscTrack(genome="hg19", chromosome = "chr12", table="ncbiRefSeq",
track = 'NCBI RefSeq', trackType="GeneRegionTrack",
rstarts = "exonStarts", rends = "exonEnds", gene = "name",
symbol = 'name', transcript = "name", strand = "strand",
name = "RefSeq", stacking = 'pack', showID = T,
geneSymbol = T, transcriptAnnotation="symbol")
# Warning message:
# In .local(x, ...) :
# 'track' parameter is deprecated now you go by the 'table' instead
# Use ucscTables(genome, track) to retrieve the list of tables for a track
ucscGenes
# GeneRegionTrack 'RefSeq'
# | genome: hg19
# | active chromosome: chr12
# | annotation features: 48884> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.11.0
LAPACK: /usr/lib/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Kolkata
tzcode source: system (glibc)
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Gviz_1.46.1 GenomicRanges_1.54.1 GenomeInfoDb_1.38.1
[4] IRanges_2.36.0 S4Vectors_0.40.1 BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] DBI_1.1.3 bitops_1.0-7
[3] deldir_2.0-2 gridExtra_2.3
[5] biomaRt_2.58.0 rlang_1.1.2
[7] magrittr_2.0.3 biovizBase_1.50.0
[9] matrixStats_1.1.0 compiler_4.3.2
[11] RSQLite_2.3.3 GenomicFeatures_1.54.1
[13] png_0.1-8 vctrs_0.6.4
[15] ProtGenerics_1.34.0 stringr_1.5.1
[17] pkgconfig_2.0.3 crayon_1.5.2
[19] fastmap_1.1.1 backports_1.4.1
[21] dbplyr_2.4.0 XVector_0.42.0
[23] utf8_1.2.4 Rsamtools_2.18.0
[25] rmarkdown_2.25 bit_4.0.5
[27] xfun_0.41 zlibbioc_1.48.0
[29] cachem_1.0.8 progress_1.2.2
[31] blob_1.2.4 DelayedArray_0.28.0
[33] BiocParallel_1.36.0 jpeg_0.1-10
[35] parallel_4.3.2 prettyunits_1.2.0
[37] cluster_2.1.4 VariantAnnotation_1.48.1
[39] R6_2.5.1 stringi_1.8.2
[41] RColorBrewer_1.1-3 rtracklayer_1.62.0
[43] rpart_4.1.21 Rcpp_1.0.11
[45] SummarizedExperiment_1.32.0 knitr_1.45
[47] base64enc_0.1-3 Matrix_1.6-3
[49] nnet_7.3-19 tidyselect_1.2.0
[51] rstudioapi_0.15.0 dichromat_2.0-0.1
[53] abind_1.4-5 yaml_2.3.7
[55] codetools_0.2-19 curl_5.1.0
[57] lattice_0.22-5 tibble_3.2.1
[59] Biobase_2.62.0 KEGGREST_1.42.0
[61] evaluate_0.23 foreign_0.8-85
[63] BiocFileCache_2.10.1 xml2_1.3.5
[65] Biostrings_2.70.1 pillar_1.9.0
[67] filelock_1.0.2 MatrixGenerics_1.14.0
[69] checkmate_2.3.0 generics_0.1.3
[71] RCurl_1.98-1.13 ensembldb_2.26.0
[73] hms_1.1.3 ggplot2_3.4.4
[75] munsell_0.5.0 scales_1.2.1
[77] glue_1.6.2 lazyeval_0.2.2
[79] Hmisc_5.1-1 tools_4.3.2
[81] interp_1.1-4 BiocIO_1.12.0
[83] data.table_1.14.8 BSgenome_1.70.1
[85] GenomicAlignments_1.38.0 XML_3.99-0.14
[87] latticeExtra_0.6-30 AnnotationDbi_1.64.1
[89] colorspace_2.1-0 GenomeInfoDbData_1.2.11
[91] htmlTable_2.4.2 restfulr_0.0.15
[93] Formula_1.2-5 cli_3.6.1
[95] rappdirs_0.3.3 fansi_1.0.5
[97] S4Arrays_1.2.0 dplyr_1.1.4
[99] AnnotationFilter_1.26.0 gtable_0.3.4
[101] digest_0.6.33 SparseArray_1.2.2
[103] rjson_0.2.21 htmlwidgets_1.6.3
[105] memoise_2.0.1 htmltools_0.5.7
[107] lifecycle_1.0.4 httr_1.4.7
[109] bit64_4.0.5
Hi,
I'm using the command in R
ucscGenes <- UcscTrack(genome="hg19", chromosome = "chr12", table="ncbiRefSeq", track = 'NCBI RefSeq', trackType="GeneRegionTrack", rstarts = "exonStarts", rends = "exonEnds", gene = "name", symbol = 'name', transcript = "name", strand = "strand", name = "RefSeq", stacking = 'pack', showID = T, geneSymbol = T, transcriptAnnotation="symbol")
And I keep getting this error : Error in normArgTrack(track, trackids) : Unknown track: refSeqComposite
I checked the table and the track, both of them exist and are available at https://genome.ucsc.edu/cgi-bin/hgTables
Here is my sessionInfo()
R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4.1
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
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: America/New_York tzcode source: internal
attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] org.Hs.eg.db_3.18.0 AnnotationDbi_1.64.1 Biobase_2.62.0 rtracklayer_1.62.0 Gviz_1.46.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.1 IRanges_2.36.0
[9] S4Vectors_0.40.1 BiocGenerics_0.48.1
loaded via a namespace (and not attached): [1] DBI_1.1.3 bitops_1.0-7 deldir_1.0-9 gridExtra_2.3 biomaRt_2.58.0 rlang_1.1.2
[7] magrittr_2.0.3 biovizBase_1.50.0 matrixStats_1.1.0 compiler_4.3.0 RSQLite_2.3.3 GenomicFeatures_1.54.1
[13] png_0.1-8 vctrs_0.6.4 ProtGenerics_1.34.0 stringr_1.5.0 pkgconfig_2.0.3 crayon_1.5.2
[19] fastmap_1.1.1 backports_1.4.1 dbplyr_2.4.0 XVector_0.42.0 utf8_1.2.4 Rsamtools_2.18.0
[25] rmarkdown_2.25 bit_4.0.5 xfun_0.41 zlibbioc_1.48.0 cachem_1.0.8 progress_1.2.2
[31] blob_1.2.4 DelayedArray_0.28.0 BiocParallel_1.36.0 jpeg_0.1-10 parallel_4.3.0 prettyunits_1.2.0
[37] cluster_2.1.4 VariantAnnotation_1.48.0 R6_2.5.1 stringi_1.8.1 RColorBrewer_1.1-3 rpart_4.1.21
[43] Rcpp_1.0.11 SummarizedExperiment_1.32.0 knitr_1.45 base64enc_0.1-3 Matrix_1.6-1.1 nnet_7.3-19
[49] tidyselect_1.2.0 rstudioapi_0.15.0 dichromat_2.0-0.1 abind_1.4-5 yaml_2.3.7 codetools_0.2-19
[55] curl_5.1.0 lattice_0.22-5 tibble_3.2.1 KEGGREST_1.42.0 evaluate_0.23 foreign_0.8-85
[61] BiocFileCache_2.10.1 xml2_1.3.5 Biostrings_2.70.1 pillar_1.9.0 BiocManager_1.30.22 filelock_1.0.2
[67] MatrixGenerics_1.14.0 checkmate_2.3.0 generics_0.1.3 RCurl_1.98-1.13 ensembldb_2.26.0 hms_1.1.3
[73] ggplot2_3.4.4 munsell_0.5.0 scales_1.2.1 glue_1.6.2 lazyeval_0.2.2 Hmisc_5.1-1
[79] tools_4.3.0 interp_1.1-4 BiocIO_1.12.0 data.table_1.14.8 BSgenome_1.70.1 GenomicAlignments_1.38.0
[85] XML_3.99-0.15 latticeExtra_0.6-30 colorspace_2.1-0 GenomeInfoDbData_1.2.11 htmlTable_2.4.2 restfulr_0.0.15
[91] Formula_1.2-5 cli_3.6.1 rappdirs_0.3.3 fansi_1.0.5 S4Arrays_1.2.0 dplyr_1.1.3
[97] AnnotationFilter_1.26.0 gtable_0.3.4 digest_0.6.33 SparseArray_1.2.2 rjson_0.2.21 htmlwidgets_1.6.2
[103] memoise_2.0.1 htmltools_0.5.7 lifecycle_1.0.4 httr_1.4.7 bit64_4.0.5
I talked with UC Santa Cruz Genomics Institute and they said that the rtracklayer package is maintained by you. They said that the problem appears to be an issue with the request rtracklayer is sending to the UCSC Genome Browser.
Best, Paulo Cordeiro