[BioC] Gviz import bed file for AnnotationTrack

[Hahne, Florian]

Should be fixed now in version 1.4.4
Florian

On 6/27/13 2:48 AM, "Christopher DeBoever" <cdeboeve at ucsd.edu> wrote:

>Hi all, I'm trying to import a bed file into Gviz and getting an error
>(see
>below). Has anyone encountered this error?
>
>Thanks,
>
>Chris DeBoever
>
>Frazer Laboratory
>Bioinformatics and Systems Biology
>University of California San Diego
>
>> library(Gviz)
>Loading required package: grid
>> atrack = AnnotationTrack("test3.bed",genome="hg19")
>Error in .local(range, ...) : object 'cmpa' not found
>> sessionInfo()
>R version 3.0.1 (2013-05-16)
>Platform: x86_64-apple-darwin10.8.0 (64-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] grid      stats     graphics  grDevices utils     datasets  methods
>[8] base
>
>other attached packages:
>[1] Gviz_1.4.2
>
>loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.22.6   Biobase_2.20.0         BiocGenerics_0.6.0
> [4] biomaRt_2.16.0         Biostrings_2.28.0      biovizBase_1.8.1
> [7] bitops_1.0-5           BSgenome_1.28.0        cluster_1.14.4
>[10] colorspace_1.2-2       DBI_0.2-7              dichromat_2.0-0
>[13] GenomicFeatures_1.12.2 GenomicRanges_1.12.4   Hmisc_3.10-1.1
>[16] IRanges_1.18.1         labeling_0.2           lattice_0.20-15
>[19] munsell_0.4            parallel_3.0.1         plyr_1.8
>[22] RColorBrewer_1.0-5     RCurl_1.95-4.1         Rsamtools_1.12.3
>[25] RSQLite_0.11.4         rtracklayer_1.20.2     scales_0.2.3
>[28] stats4_3.0.1           stringr_0.6.2          tools_3.0.1
>[31] XML_3.95-0.2           zlibbioc_1.6.0
>>
>
>Example lines from bed file:
>
>chr22 23229959 23230008 f1 0
>chr9 2653832 2654480 f2 0
>
>	[[alternative HTML version deleted]]
>
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