[BioC] Gviz UcscTrack error

[Anna Sawicka]

Dear Florian,
thank you for the response. Everything works today. This must have been a server problem. And thanks a lot for you suggestion concerning RefSeq gene models!
Best wishes,
Ania

> Hi Ania,
> I can't seem to reproduce your problem here:
>> library(Gviz)
> Loading required package: grid
>> genetrack=UcscTrack(track="RefSeq Genes", table="refGene",
> 
> +                     trackType="GeneRegionTrack",chromosome="chr5",
> genome="mm9",
> +                     rstart="exonStarts", rends="exonEnds", gene="name",
> symbol="name2",
> +                     transcript="name", strand="strand", name="RefSeq
> Genes", feature="name2",
> +                     showId=T, from=30334169, to=30349988, fill = "green")
>> sessionInfo()
> R version 3.0.2 Patched (2013-10-27 r64116)
> Platform: i386-apple-darwin12.5.0/i386 (32-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] parallel  grid      stats     graphics  grDevices utils     datasets
> [8] methods   base 
> 
> other attached packages:
> [1] GenomicFeatures_1.14.2 AnnotationDbi_1.24.0   Biobase_2.22.0
> [4] GenomicRanges_1.14.4   XVector_0.2.0          IRanges_1.20.6
> [7] BiocGenerics_0.8.0     Gviz_1.6.0             BiocInstaller_1.12.0
> 
> loaded via a namespace (and not attached):
> [1] biomaRt_2.18.0      Biostrings_2.30.1   biovizBase_1.10.7
> [4] bitops_1.0-6        BSgenome_1.30.0     cluster_1.14.4
> [7] colorspace_1.2-4    DBI_0.2-7           dichromat_2.0-0
> [10] Formula_1.1-1       Hmisc_3.13-0        labeling_0.2
> [13] lattice_0.20-24     latticeExtra_0.6-26 munsell_0.4.2
> [16] plyr_1.8            RColorBrewer_1.0-5  RCurl_1.95-4.1
> [19] Rsamtools_1.14.2    RSQLite_0.11.4      rtracklayer_1.22.0
> [22] scales_0.2.3        splines_3.0.2       stats4_3.0.2
> [25] stringr_0.6.2       survival_2.37-4     tools_3.0.2
> [28] XML_3.98-1.1        zlibbioc_1.8.0
> 
> Maybe the UCSC server had some issue on the day you tried this? Could you
> please check again today whether the problem has gone away? Both Gviz and
> rtracklayer versions are the same on my machine and yours, so package
> versions should not be an issue. The only difference I see in the
> sessionInfo is a slightly newer R version in my end (3.0.2 Patched)
> 
> If all that you are interested in are RefSeq gene models from UCSC you
> might as well consider building a GeneRegionTrack directly from a
> TranscriptDB object. This should be much more efficient and you will also
> get UTR information for free. Please see the package vignette for details.
> 
> Florian
> 
> 
> 
> 
> 
> 
> On 1/7/14 10:44 PM, "Anna Sawicka [guest]" <guest at bioconductor.org> wrote:
> 
>> genetrack=UcscTrack(track="RefSeq Genes", table="refGene",
>>                   trackType="GeneRegionTrack",chromosome="chr5",
>> genome="mm9",
>>                   rstart="exonStarts", rends="exonEnds", gene="name",
>> symbol="name2",
>>                   transcript="name", strand="strand", name="RefSeq
>> Genes", feature="name2",
>>                   showId=T, from=30334169, to=30349988, fill = "green")
>