Sorry about this. Should be fixed with rtracklayer 1.13.8. Michael
On Thu, Jul 14, 2011 at 9:05 AM, Jason Lu <jasonl...@gmail.com> wrote: > Hi list, > > I tried to get refseq coordinates here. It has been working well but I > encountered the following error message today. > > library(GenomicFeatures) > txdb <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene") > Error in tableNames(ucscTableQuery(session, track = track)) : > error in evaluating the argument 'object' in selecting a method for > function 'tableNames': Error in GRangesForGenome(range, > seqlengths(session)) : > Chromosome(s) 249250621, 106433, 547496, 243199373, 198022430, > 191154276, 590426, 189789, 191469, 180915260, 171115067, 4622290, > 4795371, 4610396, 4683263, 4833398, 4611984, 4928567, 159138663, > 182896, 146364022, 38914, 37175, 141213431, 90085, 169874, 187035, > 36148, 135534747, 135006516, 40103, 133851895, 115169878, 107349540, > 102531392, 90354753, 81195210, 1680828, 37498, 81310, 174588, 41001, > 78077248, 4262, 59128983, 92689, 159169, 63025520, 48129895, 27682, > 51304566, 155270560, 59373566, 166566, 186858, 164239, 137718, 172545, > 172294, 172149, 161147, 179198, 161802, 155397, 186861, 180455, > 179693, 211173, 15008, 128374, 129120, 19913, 43691, 27386, 40652, > 45941, 40531, 34474, 41934, 45867, 39939, 33824, 41933, 42152, 43523, > 43341, 39929, 36651, 38154, 36422, 39786, 38502, 16571are invalid for: > hg19 > > > > sessionInfo() > R version 2.14.0 Under development (unstable) (2011-04-26 r55655) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] Rsamtools_1.5.38 Biostrings_2.21.6 GenomicFeatures_1.5.14 > [4] GenomicRanges_1.5.17 IRanges_1.11.11 > > loaded via a namespace (and not attached): > [1] BSgenome_1.21.3 Biobase_2.13.7 DBI_0.2-5 RCurl_1.6-6 > [5] RSQLite_0.9-4 XML_3.4-0 biomaRt_2.9.2 > rtracklayer_1.13.7 > [9] tools_2.14.0 zlibbioc_0.1.7 > > Thanks for any suggestions. > > Jason > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
