[BioC] How to get closest gene around chromosome location?[biomaRt]

João Fadista Joao.Fadista at agrsci.dk
Tue Oct 28 09:57:31 CET 2008

Hi Sean,

Concerning the getRefflat function, I can´t seem to get it to work with bos taurus nor human. Is it because I am having R version 2.6.0? 

> rf <- getRefflat('bosTau4')
trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/database/refFlat.txt.gz'
Content type 'application/x-gzip' length 906439 bytes (885 Kb)
opened URL
downloaded 885 Kb

Error in pushBack(c(lines, lines), file) : 
  can only push back on text-mode connections
> sessionInfo()
R version 2.6.0 (2007-10-03) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ACME_1.8.0

Best regards,
João Fadista


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis
Sent: Monday, October 27, 2008 7:24 PM
To: Hooiveld, Guido
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] How to get closest gene around chromosome location?[biomaRt]

On Mon, Oct 27, 2008 at 12:45 PM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Dear list,
> Anyone a pointer / piece of code on how to find genes that are closest 
> to a specific chromosomal location?
> I am using Biostrings and associated mouse genome package to find and 
> localize specific sequences (putative TFBS). This works fine (thanks 
> Herve for the clear vignette). I have now an output (list) like this:
> seqname start  end  strand patternID
> chr1 7196884  7196895  +  GH_TEST
> chr1 15433465 15433476 +  GH_TEST
> chr1 78251474 78251485 +  GH_TEST
> chr1 82635484 82635495 +  GH_TEST
> chr1 22603411 22603422 -  GH_TEST
> chr1 34167820 34167831 -  GH_TEST
> chr1 47227452 47227463 -  GH_TEST
> Next I would like to know which gene is closest to the each entry, and 
> what the distance is.
> For example, info like the first entry is situated 1234 bp upstream of 
> the TSS of gene ENSMUSG000xx, and entry 2 is located 3456 bp 
> downstream of the TSS of gene ENSMUSG00yy. Etc.
> I am thinking of using BiomaRt for this, but I don't know how to do 
> this.
> Note: In the archive I did find a related thread but the functions 
> given unfortunately do not give the info I am after.
> http://article.gmane.org/gmane.science.biology.informatics.conductor/5
> 09
> 7
> Any suggestions are appreciated,

The findClosestGene() function in the ACME package will do this using RefSeq data from UCSC.


Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list