Hi there, I am using for the first time rtracklayer and I'm following the Vignette with my own SNP data. I am just testing it, so the task was simple, i.e. visualising the position of a list of novel snps. I converted a GRanges object in a data frame first, in order to follow step by step the Vignette and reproduce the workflow, as it follows, but as you can see I get this error which I can't find a way out for. Thanks for your help, Francesco > novel.data<-as.data.frame(novel.snps) > novel.data<-cbind(novel.data,name=row.names(novel.data)) > head(novel.data) seqnames start end width strand ALT name chr22:17468875 chr22 17468875 17468875 1 * T chr22:17468875 chr22:17468918 chr22 17468918 17468918 1 * A chr22:17468918 chr22:18222132 chr22 18222132 18222132 1 * G chr22:18222132 chr22:18226601 chr22 18226601 18226601 1 * G chr22:18226601 chr22:18918666 chr22 18918666 18918666 1 * C chr22:18918666 chr22:19026331 chr22 19026331 19026331 1 * C chr22:19026331 > targetRanges <-IRanges(novel.data$start, novel.data$end) > targetRanges IRanges of length 159 start end width [1] 17468875 17468875 1 [2] 17468918 17468918 1 [3] 18222132 18222132 1 [4] 18226601 18226601 1 [5] 18918666 18918666 1 [6] 19026331 19026331 1 [7] 19026374 19026374 1 [8] 19165264 19165264 1 [9] 19438111 19438111 1 > targetTrack <- with(novel.data, + GRangesForUCSCGenome("hg19",seqnames,targetRanges,strand,name)) > session <- browserSession("UCSC") > track(session,"novels") <- targetTrack Error in genome(seqinfo(x)) : error in evaluating the argument 'x' in selecting a method for function 'genome': Error in .normargSeqlengths(seqlengths, seqnames) : length of supplied 'seqlengths' must equal the number of sequences I am using R-devel because I need some new features of VariantAnnotation > sessionInfo() R Under development (unstable) (2012-01-20 r58146) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.15.6 GenomeGraphs_1.15.0 biomaRt_2.11.1 SNPlocs.Hsapiens.dbSNP.20110815_0.99.6 [5] BSgenome.Hsapiens.UCSC.hg19_1.3.17 BSgenome_1.23.2 TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 GenomicFeatures_1.7.10 [9] VariantAnnotation_1.1.30 Rsamtools_1.7.22 Biostrings_2.23.5 AnnotationDbi_1.17.11 [13] Biobase_2.15.3 GenomicRanges_1.7.15 IRanges_1.13.20 BiocGenerics_0.1.4 loaded via a namespace (and not attached): [1] DBI_0.2-5 Matrix_1.0-3 RCurl_1.9-5 RSQLite_0.11.1 XML_3.8-0 bitops_1.0-4.1 lattice_0.20-0 snpStats_1.5.2 splines_2.15.0 [10] survival_2.36-10 tools_2.15.0 zlibbioc_1.1.0 [[alternative HTML version deleted]]

Thanks, I am working on fixing this bug. Even with that fixed though, the function is not likely to work anyway; the interface to the UCSC browser is broken. Sorry, Michael On Fri, Jan 27, 2012 at 9:16 AM, Lescai, Francesco <f.lescai@ucl.ac.uk>wrote: > Hi there, > I am using for the first time rtracklayer and I'm following the Vignette > with my own SNP data. > I am just testing it, so the task was simple, i.e. visualising the > position of a list of novel snps. > > I converted a GRanges object in a data frame first, in order to follow > step by step the Vignette and reproduce the workflow, as it follows, but as > you can see I get this error which I can't find a way out for. > Thanks for your help, > Francesco > > > novel.data<-as.data.frame(novel.snps) > > novel.data<-cbind(novel.data,name=row.names(novel.data)) > > head(novel.data) > seqnames start end width strand ALT name > chr22:17468875 chr22 17468875 17468875 1 * T chr22:17468875 > chr22:17468918 chr22 17468918 17468918 1 * A chr22:17468918 > chr22:18222132 chr22 18222132 18222132 1 * G chr22:18222132 > chr22:18226601 chr22 18226601 18226601 1 * G chr22:18226601 > chr22:18918666 chr22 18918666 18918666 1 * C chr22:18918666 > chr22:19026331 chr22 19026331 19026331 1 * C chr22:19026331 > > targetRanges <-IRanges(novel.data$start, novel.data$end) > > targetRanges > IRanges of length 159 > start end width > [1] 17468875 17468875 1 > [2] 17468918 17468918 1 > [3] 18222132 18222132 1 > [4] 18226601 18226601 1 > [5] 18918666 18918666 1 > [6] 19026331 19026331 1 > [7] 19026374 19026374 1 > [8] 19165264 19165264 1 > [9] 19438111 19438111 1 > > > targetTrack <- with(novel.data, > + > GRangesForUCSCGenome("hg19",seqnames,targetRanges,strand,name)) > > session <- browserSession("UCSC") > > track(session,"novels") <- targetTrack > Error in genome(seqinfo(x)) : > error in evaluating the argument 'x' in selecting a method for function > 'genome': Error in .normargSeqlengths(seqlengths, seqnames) : > length of supplied 'seqlengths' must equal the number of sequences > > I am using R-devel because I need some new features of VariantAnnotation > > > sessionInfo() > R Under development (unstable) (2012-01-20 r58146) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] rtracklayer_1.15.6 GenomeGraphs_1.15.0 > biomaRt_2.11.1 > SNPlocs.Hsapiens.dbSNP.20110815_0.99.6 > [5] BSgenome.Hsapiens.UCSC.hg19_1.3.17 BSgenome_1.23.2 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 GenomicFeatures_1.7.10 > [9] VariantAnnotation_1.1.30 Rsamtools_1.7.22 > Biostrings_2.23.5 AnnotationDbi_1.17.11 > [13] Biobase_2.15.3 GenomicRanges_1.7.15 > IRanges_1.13.20 BiocGenerics_0.1.4 > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 Matrix_1.0-3 RCurl_1.9-5 RSQLite_0.11.1 > XML_3.8-0 bitops_1.0-4.1 lattice_0.20-0 snpStats_1.5.2 > splines_2.15.0 > [10] survival_2.36-10 tools_2.15.0 zlibbioc_1.1.0 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]