[BioC] Gviz

[Hahne, Florian]

Hi Fiorella,
you can do this filtering directly in the constructor function. Take a
look at the 'filters' argument in the help page for the
BiomartGeneRegionTrack class. It's value is directly forwarded to
biomaRt's getBM function, so it's documentation as well as 'listFilters'
might also be instructive. Your particular case would probably boil down
to something like this:

biomTrack <- BiomartGeneRegionTrack(genome = "hg19", chromosome = chr,
start = 63038367 , end = 64536346, name = "ENSEMBLE",
filters=list(biotype="protein_coding")

I find it quite useful when creating more complex biomaRt queries to first
construct something similar in the web interface and then look at the XML
representation of the query (there is a button for it)

Hope that helps,
Florian


Florian Hahne
Novartis Institute For Biomedical Research
Translational Sciences / Preclinical Safety / PCS Informatics
Expert Data Integration and Modeling Bioinformatics
CHBS, WKL-135.2.26
Novartis Institute For Biomedical Research, Werk Klybeck
Klybeckstrasse 141
CH-4057 Basel
Switzerland
Phone: +41 61 6967127
Email : florian.hahne at novartis.com




On 5/14/13 3:45 PM, "Fiorella Schischlik [guest]" <guest at bioconductor.org>
wrote:

>63038367