makeTranscriptDbFromUCSC
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Georg Otto ▴ 120
@georg-otto-6333
Last seen 5.4 years ago
United Kingdom
Dear Bioconductors, I am trying to use makeTranscriptDbFromUCSC() from the GenomicFeatures, but it results in an error: > txdb.ensgene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene") Error in tableNames(ucscTableQuery(session, track = track)) : error in evaluating the argument 'object' in selecting a method for function 'tableNames': Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 2 elements However a query for hg18 works fine: > txdb.ensgene <- makeTranscriptDbFromUCSC(genome = "hg18", tablename = "ensGene") Download the ensGene table ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TranscriptDb object ... OK Any idea what is going on? Best wishes, Georg > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] Rsamtools_1.14.2 Biostrings_2.30.1 rtracklayer_1.22.0 [4] pamr_1.54.1 survival_2.37-4 cluster_1.14.4 [7] RColorBrewer_1.0-5 gplots_2.12.1 xtable_1.7-1 [10] scatterplot3d_0.3-34 plyr_1.8 org.Hs.eg.db_2.10.1 [13] goseq_1.14.0 geneLenDataBase_0.99.12 BiasedUrn_1.06.1 [16] edgeR_3.4.2 limma_3.18.7 biomaRt_2.18.0 [19] KEGG.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7 [22] GenomicFeatures_1.14.2 AnnotationDbi_1.24.0 GenomicRanges_1.14.4 [25] XVector_0.2.0 IRanges_1.20.6 DESeq_1.14.0 [28] lattice_0.20-24 locfit_1.5-9.1 Biobase_2.22.0 [31] BiocGenerics_0.8.0 corrplot_0.73 loaded via a namespace (and not attached): [1] annotate_1.40.0 bitops_1.0-6 BSgenome_1.30.0 caTools_1.16 [5] compiler_3.0.1 gdata_2.13.2 genefilter_1.44.0 geneplotter_1.40.0 [9] grid_3.0.1 gtools_3.1.1 KernSmooth_2.23-10 Matrix_1.1-0 [13] mgcv_1.7-27 nlme_3.1-113 RCurl_1.95-4.1 stats4_3.0.1 [17] tcltk_3.0.1 tools_3.0.1 XML_3.98-1.1 zlibbioc_1.8.0
TranscriptDb TranscriptDb • 2.0k views
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Entering edit mode
Georg Otto ▴ 120
@georg-otto-6333
Last seen 5.4 years ago
United Kingdom
Please ignore this message, it works again. Cheers, Georg Georg Otto <georg.otto at="" imm.ox.ac.uk=""> writes: > Dear Bioconductors, > > I am trying to use makeTranscriptDbFromUCSC() from the GenomicFeatures, > but it results in an error: > >> txdb.ensgene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene") > > Error in tableNames(ucscTableQuery(session, track = track)) : > error in evaluating the argument 'object' in selecting a method for > function 'tableNames': Error in scan(file, what, nmax, sep, dec, quote, > skip, nlines, na.strings, : > line 1 did not have 2 elements > > However a query for hg18 works fine: > > > >> txdb.ensgene <- makeTranscriptDbFromUCSC(genome = "hg18", tablename = "ensGene") > Download the ensGene table ... OK > Extract the 'transcripts' data frame ... OK > Extract the 'splicings' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TranscriptDb object ... OK > > Any idea what is going on? > > Best wishes, > > Georg > > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] splines parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] Rsamtools_1.14.2 Biostrings_2.30.1 rtracklayer_1.22.0 > [4] pamr_1.54.1 survival_2.37-4 cluster_1.14.4 > [7] RColorBrewer_1.0-5 gplots_2.12.1 xtable_1.7-1 > [10] scatterplot3d_0.3-34 plyr_1.8 org.Hs.eg.db_2.10.1 > [13] goseq_1.14.0 geneLenDataBase_0.99.12 BiasedUrn_1.06.1 > [16] edgeR_3.4.2 limma_3.18.7 biomaRt_2.18.0 > [19] KEGG.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7 > [22] GenomicFeatures_1.14.2 AnnotationDbi_1.24.0 GenomicRanges_1.14.4 > [25] XVector_0.2.0 IRanges_1.20.6 DESeq_1.14.0 > [28] lattice_0.20-24 locfit_1.5-9.1 Biobase_2.22.0 > [31] BiocGenerics_0.8.0 corrplot_0.73 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 bitops_1.0-6 BSgenome_1.30.0 caTools_1.16 > [5] compiler_3.0.1 gdata_2.13.2 genefilter_1.44.0 geneplotter_1.40.0 > [9] grid_3.0.1 gtools_3.1.1 KernSmooth_2.23-10 Matrix_1.1-0 > [13] mgcv_1.7-27 nlme_3.1-113 RCurl_1.95-4.1 stats4_3.0.1 > [17] tcltk_3.0.1 tools_3.0.1 XML_3.98-1.1 zlibbioc_1.8.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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