gviz: BiomartGeneRegionTrack throws an error
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tonja.r ▴ 80
@tonjar-7565
Last seen 7.5 years ago
United Kingdom

Gviz_1.10.11
biomaRt_2.22.0  

I want to use BiomartGeneRegionTrack from GVIZ but it throws me an error. I am quite familiar with biomart and normally this error means that the attribute that I am trying to call (which served as an example in user guide) is invalid.

chr = "chr6"
biomTrack <- BiomartGeneRegionTrack(genome = "hg19", chromosome = chr, start = 20000000, end = 21000000, name = "ENSEMBL")

Fehler in getBM(attributes, filters = filterNames, values = filterValues,  :
  Invalid attribute(s): external_gene_id
Please use the function 'listAttributes' to get valid attribute names

 

How should a BiomartGeneRegionTrack be called?

This also produces an error:

> bm <- useMart(host="oct2012.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL",
+               dataset="hsapiens_gene_ensembl")
> fm <- Gviz:::.getBMFeatureMap()
Fehler in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  Objekt '.getBMFeatureMap' nicht gefunden

 


 

 

 

gviz biomart • 1.4k views
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@florianhahnenovartiscom-3784
Last seen 5.6 years ago
Switzerland

Please post your sessionInfo() output. Without it I can't help you. 

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