Question

Gviz GeneRegionTrack draw only one gene in the range

0

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tangming2005 ▴ 190

@tangming2005-6754

Last seen 5 months ago

United States

Hi there,

I want to draw only one gene model in one genomic range ( some genes have overlapping ranges).

How can I do it using GeneRegionTrack in the Gviz package?

I read the tutorial,

" Alternatively, one can provide the Ensembl trancript or gene id via the transcript or gene arguments, or an Entrez id via the entrez argument. In all of these cases the constructor will also fetch models for other genes that overlap the same region. If that is not desired one needs to provide an explicit Biomart filter.

biomTrack <- BiomartGeneRegionTrack(genome = "hg19", name = "ENSEMBL", symbol = "ABCB5") 
plotTracks(biomTrack)

How can I specify the filter here?

Thanks,

Ming Tang

Gviz • 3.2k views

ADD COMMENT • link updated 8.7 years ago by Robert Ivanek ▴ 730 • written 8.7 years ago by tangming2005 ▴ 190

score 2 · Accepted Answer · 2015-08-19

2

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Robert Ivanek ▴ 730

@robert-ivanek-5892

Last seen 4 months ago

Switzerland

Please have a look on the documentation of the getBM function from biomaRt package how to specify the filters. Here is an example how you can list all available filters for human genome:

library(biomaRt)
mart <- useMart("ensembl")
mart <- useDataset("hsapiens_gene_ensembl",mart)
listFilters(mart)

The one you are probably interested in is the following:

listFilters(mart)[70,]

So the call in Gviz can look like this:

library(Gviz)
biomTrack <- BiomartGeneRegionTrack(genome = "hg19", name = "ENSEMBL", symbol = "ABCB5", transcriptAnnotation = "symbol", filters=list(hgnc_symbol="ABCB5"))
plotTracks(biomTrack)

ADD COMMENT • link 8.7 years ago Robert Ivanek ▴ 730

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Thanks for your answer. It solved my question. Now I want only one specific transcript, but it gave an error. I checked that

with_ens_hs_transcript is a valid filter.

biomTrack <- BiomartGeneRegionTrack(genome = "hg19", name = "ENSEMBL", symbol = "KIT",
+                                     filters=list(with_ens_hs_transcript="ENST00000288135"))
Error in getBM(as.vector(featureMap), filters = names(filterValues), values = filterValues,  : 
  Invalid filters(s): with_ens_hs_transcript 
Please use the function 'listFilters' to get valid filter names

ADD REPLY • link 8.7 years ago tangming2005 ▴ 190

1

Entering edit mode

I am not a biomaRt expert but I would say that the filter "with_ens_hs_transcript" is used to restrict the output only to items with Ensembl Human Transcript IDs but you cannot use it to filter for specific transcript it. For that you need to use filter called "ensembl_transcript_id". Something like this might work for you:

biomTrack <- BiomartGeneRegionTrack(genome = "hg19", name = "ENSEMBL", symbol = "KIT", filters=list(ensembl_transcript_id="ENST00000288135"))