[Bioc-devel] BiomartGeneRegionTrack question
Obenchain, Valerie
Valerie.Obenchain at roswellpark.org
Tue Jul 26 21:27:04 CEST 2016
Hi Florian,
On 07/21/2016 01:47 AM, Hahne, Florian wrote:
> This is a problem with the biomaRt package and its connection to the Ensembl archives, not Gviz. Here’s the call the fails:
> listMarts(host="feb2012.archive.ensembl.org", path="/biomart/martservice")
>
> It looks like Ensembl is no longer providing a download for the feb2012 archive. You could try the May2012 one, which according to this table (http://www.ensembl.org/info/website/archives/assembly.html) should still provide the mm9 (NCBIm37) genome:
>
> bm <- useMart(host = "may2012.archive.ensembl.org", biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl")
> bmTrack <- BiomartGeneRegionTrack(start=26682683, end=26711643, chromosome=7, genome="mm9", biomart = bm)
>
> I’ll update the automated mapping from UCSC genome identifier to Biomart within Gviz, however I am more and more convinced that this whole setup is not ideal. I simply do not have the time to keep track of all the Ensembl changes and new genome versions. There really should be an annotation package or the like maintained by Bioconductor core or within the biomaRt package that gives a mapping from a UCSC genome identifier to an Ensembl genome version and the Ensembl archive to access that.
The mapping between genome identifiers seems like a natural fit for the
GenomeInfoDb package. Mapping to a particular ensembl archive might be
more appropriate to have in biomaRt but I'm open to what people think.
If you're in favor of this re-org we can start incorporating the
following into GenomeInfoDb:
- Gviz:::.getBiobmart() # or move to biomaRt
- Gviz:::.ucsc2Ensembl()
- extdata/biomartVersionsNow.txt
- extdata/biomartVersionsLatest.txt
Any hints or tips for maintaining the .txt files, i.e., what worked,
what you might do different the second time around?
Valerie
>
> Florian
>
>
> On 20/07/16 21:15, "Bioc-devel on behalf of James W. MacDonald" <bioc-devel-bounces at r-project.org on behalf of jmacdon at uw.edu> wrote:
>
>> Hi Holly,
>>
>> This list is intended for those that are developing packages. Your question
>> should be asked on the support site (https://support.bioconductor.org).
>> Please repost over there.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On Wed, Jul 20, 2016 at 2:04 PM, Holly <xyang2 at uchicago.edu> wrote:
>>
>>> Dear Bioconductor helpers,
>>> I am trying to plot a region of interest using the Gviz package.
>>> I met error when running the following example code:
>>>> library(Gviz)
>>>> library(GenomicRanges)
>>>> bmTrack <- BiomartGeneRegionTrack(start=26682683, end=26711643,
>>> + chromosome=7, genome="mm9")
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>>> 4: Entity 'nbsp' not defined
>>> 5: Entity 'raquo' not defined
>>> 6: Entity 'hellip' not defined
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>>> 10: Entity 'hellip' not defined
>>> 11: Opening and ending tag mismatch: img line 68 and li
>>> 12: Opening and ending tag mismatch: li line 68 and ul
>>> 13: Opening and ending tag mismatch: ul line 67 and div
>>> 14: Entity 'copy' not defined
>>> 15: Opening and ending tag mismatch: div line 19 and body
>>> 16: Opening and ending tag mismatch: body line 17 and html
>>> 17: Premature end of data in tag html line 2
>>>> sessionInfo()
>>> R version 3.3.1 (2016-06-21)
>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>> Running under: Windows 7 x64 (build 7601) Service Pack 1
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252
>>> [2] LC_CTYPE=English_United States.1252
>>> [3] LC_MONETARY=English_United States.1252
>>> [4] LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] grid parallel stats4 stats graphics grDevices utils
>>> [8] datasets methods base
>>>
>>> other attached packages:
>>> [1] Gviz_1.16.1 GenomicRanges_1.24.2 GenomeInfoDb_1.8.2
>>> [4] IRanges_2.6.1 S4Vectors_0.10.2 BiocGenerics_0.18.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] SummarizedExperiment_1.2.3 VariantAnnotation_1.18.3
>>> [3] splines_3.3.1 lattice_0.20-33
>>> [5] colorspace_1.2-6 htmltools_0.3.5
>>> [7] rtracklayer_1.32.1 GenomicFeatures_1.24.4
>>> [9] chron_2.3-47 interactiveDisplayBase_1.10.3
>>> [11] survival_2.39-5 XML_3.98-1.4
>>> [13] foreign_0.8-66 DBI_0.4-1
>>> [15] ensembldb_1.4.7 BiocParallel_1.6.2
>>> [17] RColorBrewer_1.1-2 matrixStats_0.50.2
>>> [19] plyr_1.8.4 zlibbioc_1.18.0
>>> [21] Biostrings_2.40.2 munsell_0.4.3
>>> [23] gtable_0.2.0 latticeExtra_0.6-28
>>> [25] Biobase_2.32.0 biomaRt_2.28.0
>>> [27] BiocInstaller_1.22.3 httpuv_1.3.3
>>> [29] AnnotationDbi_1.34.4 Rcpp_0.12.5
>>> [31] acepack_1.3-3.3 xtable_1.8-2
>>> [33] BSgenome_1.40.1 scales_0.4.0
>>> [35] Hmisc_3.17-4 XVector_0.12.0
>>> [37] mime_0.5 Rsamtools_1.24.0
>>> [39] gridExtra_2.2.1 AnnotationHub_2.4.2
>>> [41] ggplot2_2.1.0 digest_0.6.9
>>> [43] biovizBase_1.20.0 shiny_0.13.2
>>> [45] tools_3.3.1 bitops_1.0-6
>>> [47] RCurl_1.95-4.8 RSQLite_1.0.0
>>> [49] dichromat_2.0-0 Formula_1.2-1
>>> [51] cluster_2.0.4 Matrix_1.2-6
>>> [53] data.table_1.9.6 httr_1.2.1
>>> [55] R6_2.1.2 rpart_4.1-10
>>> [57] GenomicAlignments_1.8.4 nnet_7.3-12
>>> Thank you for help,
>>> Holly
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
>> [[alternative HTML version deleted]]
>>
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