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
>
>
>
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>
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