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

[Sean Davis]

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/509
> 7
>
> Any suggestions are appreciated,

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

Sean