Gviz : UcscTrack
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Entering edit mode
yujin ▴ 10
@25075190
Last seen 16 hours ago
South Korea

Dear all,

when I run this code (below),

`UcscTrack(genome="hg19", chromosome=chrom, track = "NCBI RefSeq", 
                table ="wgEncodeGencodeRefSeqV44lift37",
                from=minbase, to=maxbase, trackType="GeneRegionTrack", 
                rstarts="exonStarts", rends="exonEnds", gene="name", 
                symbol="name2", transcript="name", strand="strand", 
                fill="darkblue",stacking="squish", name="RefSeq",
                showId=TRUE, geneSymbol=TRUE)`

I got the error

Error in normArgTrack(track, trackids) : Unknown track: refSeqComposite In addition: 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

When I retrieve the list of tables for the track 'NCBI RefSeq, I got the below list.

[1] "ncbiRefSeq" "ncbiRefSeqCurated" [3] "ncbiRefSeqOther" "ncbiRefSeqPsl" [5] "ncbiRefSeqGenomicDiff" "refGene" [7] "ncbiRefSeqSelect" "ncbiRefSeqHgmd" [9] "all_est" "all_mrna" [11] "ccdsInfo" "hgFixed.gbCdnaInfo" [13] "hgFixed.gbMiscDiff" "hgFixed.gbSeq" [15] "hgFixed.gbWarn" "hgFixed.imageClone" [17] "hgFixed.refLink" "hgFixed.refSeqStatus" [19] "hgFixed.refSeqSummary" "kgXref" [21] "knownToRefSeq" "mrnaOrientInfo" [23] "ncbiRefSeqCds" "ncbiRefSeqLink" [25] "refFlat" "refSeqAli" [27] "seqNcbiRefSeq" "ucscRetroInfo5" [29] "wgEncodeGencodeRefSeqV24lift37" "wgEncodeGencodeRefSeqV27lift37" [31] "wgEncodeGencodeRefSeqV28lift37" "wgEncodeGencodeRefSeqV31lift37" [33] "wgEncodeGencodeRefSeqV33lift37" "wgEncodeGencodeRefSeqV34lift37" [35] "wgEncodeGencodeRefSeqV35lift37" "wgEncodeGencodeRefSeqV36lift37" [37] "wgEncodeGencodeRefSeqV37lift37" "wgEncodeGencodeRefSeqV38lift37" [39] "wgEncodeGencodeRefSeqV39lift37" "wgEncodeGencodeRefSeqV40lift37" [41] "wgEncodeGencodeRefSeqV41lift37" "wgEncodeGencodeRefSeqV42lift37" [43] "wgEncodeGencodeRefSeqV43lift37" "wgEncodeGencodeRefSeqV44lift37" [45] "xenoEst" "xenoMrna" [47] "xenoRefGene" "xenoRefSeqAli"

so that I put the 'wgEncodeGencodeRefSeqV44lift37' for the table value.

Here is my sessionInfo()

`R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.1 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Seoul tzcode source: system (glibc)

attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods
[10] base

other attached packages: [1] rtracklayer_1.62.0
[2] DMRcatedata_2.20.0
[3] ggrepel_0.9.4
[4] ggplot2_3.4.4
[5] tibble_3.2.1
[6] dplyr_1.1.3
[7] FlowSorted.Blood.EPIC_2.6.0
[8] ExperimentHub_2.10.0
[9] AnnotationHub_3.10.0
[10] BiocFileCache_2.10.1
[11] dbplyr_2.4.0
[12] stringr_1.5.0
[13] Gviz_1.46.0
[14] minfiData_0.48.0
[15] IlluminaHumanMethylation450kmanifest_0.4.0
[16] missMethyl_1.36.0
[17] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 [18] RColorBrewer_1.1-3
[19] IlluminaHumanMethylationEPICmanifest_0.3.0
[20] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 [21] minfi_1.48.0
[22] bumphunter_1.44.0
[23] locfit_1.5-9.8
[24] Biostrings_2.70.1
[25] XVector_0.42.0
[26] limma_3.58.0
[27] knitr_1.45
[28] ENmix_1.38.01
[29] SummarizedExperiment_1.32.0
[30] MatrixGenerics_1.14.0
[31] matrixStats_1.0.0
[32] doParallel_1.0.17
[33] iterators_1.0.14
[34] foreach_1.5.2
[35] mCSEA_1.22.0
[36] Homo.sapiens_1.3.1
[37] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[38] org.Hs.eg.db_3.18.0
[39] GO.db_3.18.0
[40] OrganismDbi_1.44.0
[41] GenomicFeatures_1.54.0
[42] GenomicRanges_1.54.0
[43] GenomeInfoDb_1.38.0
[44] AnnotationDbi_1.64.0
[45] IRanges_2.36.0
[46] S4Vectors_0.40.1
[47] Biobase_2.62.0
[48] BiocGenerics_0.48.0
[49] mCSEAdata_1.22.0
[50] DMRcate_2.16.0

loaded via a namespace (and not attached): [1] DSS_2.49.0 ProtGenerics_1.34.0 bitops_1.0-7
[4] httr_1.4.7 dynamicTreeCut_1.63-1 tools_4.3.1
[7] doRNG_1.8.6 backports_1.4.1 utf8_1.2.4
[10] R6_2.5.1 HDF5Array_1.30.0 lazyeval_0.2.2
[13] rhdf5filters_1.14.0 permute_0.9-7 withr_2.5.2
[16] prettyunits_1.2.0 gridExtra_2.3 base64_2.0.1
[19] preprocessCore_1.64.0 cli_3.6.1 readr_2.1.4
[22] genefilter_1.84.0 askpass_1.2.0 Rsamtools_2.18.0
[25] foreign_0.8-85 siggenes_1.76.0 illuminaio_0.44.0
[28] R.utils_2.12.2 dichromat_2.0-0.1 scrime_1.3.5
[31] BSgenome_1.70.0 readxl_1.4.3 impute_1.76.0
[34] rstudioapi_0.15.0 RSQLite_2.3.2 generics_0.1.3
[37] BiocIO_1.12.0 gtools_3.9.4 Matrix_1.6-1.1
[40] interp_1.1-4 fansi_1.0.5 abind_1.4-5
[43] R.methodsS3_1.8.2 lifecycle_1.0.3 yaml_2.3.7
[46] edgeR_4.0.0 gplots_3.1.3 rhdf5_2.46.0
[49] SparseArray_1.2.0 blob_1.2.4 promises_1.2.1
[52] crayon_1.5.2 lattice_0.22-5 annotate_1.80.0
[55] KEGGREST_1.42.0 pillar_1.9.0 beanplot_1.3.1
[58] rjson_0.2.21 codetools_0.2-19 glue_1.6.2
[61] data.table_1.14.8 vctrs_0.6.4 png_0.1-8
[64] cellranger_1.1.0 gtable_0.3.4 cachem_1.0.8
[67] xfun_0.40 S4Arrays_1.2.0 mime_0.12
[70] survival_3.5-7 statmod_1.5.0 interactiveDisplayBase_1.40.0 [73] ellipsis_0.3.2 nlme_3.1-163 bit64_4.0.5
[76] bsseq_1.38.0 progress_1.2.2 filelock_1.0.2
[79] nor1mix_1.3-0 irlba_2.3.5.1 KernSmooth_2.23-22
[82] rpart_4.1.21 colorspace_2.1-0 DBI_1.1.3
[85] Hmisc_5.1-1 nnet_7.3-19 tidyselect_1.2.0
[88] bit_4.0.5 compiler_4.3.1 curl_5.1.0
[91] graph_1.80.0 htmlTable_2.4.2 xml2_1.3.5
[94] RPMM_1.25 DelayedArray_0.28.0 caTools_1.18.2
[97] checkmate_2.3.0 scales_1.2.1 quadprog_1.5-8
[100] RBGL_1.78.0 rappdirs_0.3.3 digest_0.6.33
[103] rmarkdown_2.25 GEOquery_2.70.0 htmltools_0.5.6.1
[106] pkgconfig_2.0.3 jpeg_0.1-10 base64enc_0.1-3
[109] sparseMatrixStats_1.14.0 fastmap_1.1.1 ensembldb_2.26.0
[112] rlang_1.1.1 htmlwidgets_1.6.2 shiny_1.7.5.1
[115] DelayedMatrixStats_1.24.0 BiocParallel_1.36.0 mclust_6.0.0
[118] R.oo_1.25.0 VariantAnnotation_1.48.0 RCurl_1.98-1.12
[121] magrittr_2.0.3 Formula_1.2-5 GenomeInfoDbData_1.2.11
[124] Rhdf5lib_1.24.0 munsell_0.5.0 Rcpp_1.0.11
[127] stringi_1.7.12 zlibbioc_1.48.0 MASS_7.3-60
[130] plyr_1.8.9 deldir_1.0-9 splines_4.3.1
[133] multtest_2.58.0 hms_1.1.3 rngtools_1.5.2
[136] geneplotter_1.80.0 biomaRt_2.58.0 BiocVersion_3.18.0
[139] XML_3.99-0.14 evaluate_0.22 latticeExtra_0.6-30
[142] biovizBase_1.50.0 BiocManager_1.30.22 tzdb_0.4.0
[145] httpuv_1.6.12 tidyr_1.3.0 openssl_2.1.1
[148] purrr_1.0.2 reshape_0.8.9 xtable_1.8-4
[151] restfulr_0.0.15 AnnotationFilter_1.26.0 later_1.3.1
[154] memoise_2.0.1 GenomicAlignments_1.38.0 cluster_2.1.4 `

Could you please tell me what the problem is?

Many thanks,

Best wishes,

Yujin Kim.

rtracklayer UCSC Gviz • 416 views
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