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

[Hooiveld, Guido]

Thanks Sean for this pointer; I did not know of this function and I'll
have a look.

Guido

 

> -----Original Message-----
> From: seandavi at gmail.com [mailto:seandavi at gmail.com] On 
> Behalf Of Sean Davis
> Sent: 27 October 2008 19:24
> 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.
> 
> Sean
> 
>