[BioC] Gviz UcscTrack error

Hahne, Florian florian.hahne at novartis.com
Thu Jan 9 10:01:37 CET 2014

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",
+                     rstart="exonStarts", rends="exonEnds", gene="name",
+                     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)

[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.


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",
>                    rstart="exonStarts", rends="exonEnds", gene="name",
>                    transcript="name", strand="strand", name="RefSeq
>Genes", feature="name2",
>                    showId=T, from=30334169, to=30349988, fill = "green")

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