[BioC] How to get closest gene around chromosome location? [biomaRt]
Guido.Hooiveld at wur.nl
Mon Oct 27 22:05:10 CET 2008
Thanks Sean for this pointer; I did not know of this function and I'll
have a look.
> -----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.
> > 09
> > 7
> > Any suggestions are appreciated,
> The findClosestGene() function in the ACME package will do
> this using RefSeq data from UCSC.
More information about the Bioconductor