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