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florian.hahne@novartis.com
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@florianhahnenovartiscom-3784
Last seen 6.4 years ago
Switzerland
Hi Alejandro,
Without seeing the structure of your data table I cant be very
concrete, but in general the Gviz package should give you all the
flexibility you need in order to create a DataTrack object from it.
You may want to carefully (re-)read the section about DataTracks in
the package vignette, and also the documentation for the DataTrack()
constructor (by typing '? DataTrack). Hopefully this will already get
you much closer to a solution. If you still feel that you are stuck
after doing this home work, please send me a reduced example of your
conservation table (the first couple of rows suffice) and I can help
you with more concrete code suggestions.
Florian
-----------------------------------------------
Florian Hahne
Expert Data Integration and Bioinformatics
PCS Informatics
Novartis Pharma AG, NIBR Klybeck
Novartis Institutes for Biomed. Research
WKL-135.P.18
Klybeckstrasse 141
CH-4057 Basel
SWITZERLAND
From: Alejandro Berrío <alebesc@gmail.com<mailto:alebesc@gmail.com>>
Date: Wednesday 26 March 2014 16:51
To: Florian Hahne
<florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>>
Subject: Question on Gviz
Hello Florian,
I am so excited with the Gviz package. I like it a lot and I hope
I can make some nice genomic graphics. I was wondering if you can help
me to solve a little problem I have. Here is the thing, I am
interested in plotting a track from tabular data via converting a
phascons conservation table that I downloaded using galaxy as
xxx.tabular which then I modified at the position column from mouse
(mm9) to another species data using a MAFFT alignment.
I can plot the mm9 conservation table using UcscTrack but I cant plot
the modified table I have in my folder because this is not in a
datatrack format.
Is it possible to make the conversion?
I would appreciate any help and thanks in advance!
Cheers,
--
Alejandro Berrío, PhD Candidate
University of Texas at Austin
www.alejoberrio.com<http: www.alejoberrio.com="">
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