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

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). Martin' > > Regards, > > Prashantha Hebbar Kiradi, > Email:prashantha.hebbar at manipal.edu > Phone: +91-9886359007 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793