[BioC] Conservation tracks in BioC?

[Mercier Eloi]

Hi everyone,

I get hundreds of TF binding sites and I would be interesting to acces conservation data from UCSC.
I tried the ucscTableQuery but as mentionned Paul, there is no easy way to send multiple queries.

I tried something like :
> start=c(500,600,700)
> end=c(509,609,709)
> chr=rep("chr1",3)
> q1<- ucscTableQuery(session, "cons44way", GenomicRanges(start,end, chr))
> q1
Get track 'cons44way' within hg18:chr1:500600700-509609709

That is not what I would like.

I also tried to download the entire track by using :
> q1<- ucscTableQuery(session, "cons44way", GenomicRanges(genome="hg18"))
> q1
Get track 'cons44way' within hg18:*:*-*
> track(q1)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 100001 did not have 2 elements

Looks like the track cannot exced 99,999 lines.

So is there any easy way to send multiple queries using ucscTableQuery ?

Thanks.


On 24/09/09 9:01 PM, "Paul Leo" <p.leo at uq.edu.au> wrote:

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.

Cheers
Paul

-----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.

library("rtracklayer")
?ucscTableQuery


  Marc


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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------------------------------------------
Eloi Mercier
Computational Biology, IRCM
110 av. Des Pins O.
Montreal
Canada, QC