[BioC] Conservation tracks in BioC?

Paul Leo p.leo at uq.edu.au
Fri Sep 25 03:01:13 CEST 2009

Hi Marc,
Yes that an nice idea. 

I've got about 80K small regions across the genome, I worry that if I
can't SUM() the conservation score across each region that it would an
uncomfortably large query as the track is score per bp I think.  Anyway
I'll explore, thanks for the tip.


-----Original Message-----
From: Marc Carlson <mcarlson at fhcrc.org>
To: Paul Leo <p.leo at uq.edu.au>
Cc: bioconductor <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] Conservation tracks in BioC?
Date: Thu, 24 Sep 2009 17:10:38 -0700

Hi Paul,

Not really as an annotation package.  But there is an example of how you
can get data like this from the UCSC tables in rtracklayer.  Just load
up rtracklayer and then look at the help page for ucscTableQuery. 



Paul Leo wrote:
> Would like to get some advice on the best way to access Conservation
> data from UCSC like the human-17 way conservation etc. Now I know HOW to
> get it... ftp, table browser, SQL from UCSC.....and  I was going to
> download it and put it into an Rle object for later use. I need the lot,
> not small pieces at a time..
> My question is is it already packaged up in R-Annotation somewhere and
> I've missed it?
> Thanks
> Paul
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