[BioC] Is there any way to get upstream and downstream gene symbol?

Martin Morgan mtmorgan at fhcrc.org
Fri Dec 31 22:22:27 CET 2010

On 12/30/2010 09:54 PM, Prashantha Hebbar wrote:
> Dear Friends,
> I have to catalog upstream and downstream gene symbols of list of chromosomal 
> co-ordinates. Can you please suggest me which package in bioconductor would help 
> me to fetch up and downstream gene symbols provided chromosomal co-ordinates?

A flexible way would use IRanges::nearest, precede, and follow, where
the arguments are GenomicRanges::GRanges objects representing your
locations of interest and genes to be identified. The latter might be
created from data in the org.* packages, e.g., org.Hs.eg.db and the
org.Hs.egCHRLOC and org.Hs.egCHRLOCEND symbols, from the biomaRt
package, or from rtracklayer and UCSC. If you get stuck, show the list
what you've done with some short reproducible (i.e., pasting into a new
browser session works).

> Regards,
>  Prashantha Hebbar Kiradi,
> Email:prashantha.hebbar at manipal.edu
> Phone: +91-9886359007
> 	[[alternative HTML version deleted]]
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