Hi, I have a long list of SNP calls, like chr2.161597652 (millions of them), and would like to classify them into the following categories: 1) exon, 2) intron, 3) UTR, 4) intergenic. For the first 3 categories, it would be great if the gene name could also be identified. Can anybody point me to some function or package? Thanks. -Kunbin ______________________________________________________________________ The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to postmaster@genomichealth.com and delete this message, along with any attachments, from your computer. [[alternative HTML version deleted]]

the VariantAnnotation package is what you want. Well, assuming these are human SNPs, that is. It will also annote preceding and following genes for intergenic SNPs. On Tue, Mar 6, 2012 at 8:24 PM, Kunbin Qu <kqu@genomichealth.com> wrote: > Hi, > > I have a long list of SNP calls, like chr2.161597652 (millions of them), > and would like to classify them into the following categories: 1) exon, 2) > intron, 3) UTR, 4) intergenic. For the first 3 categories, it would be > great if the gene name could also be identified. Can anybody point me to > some function or package? Thanks. > > -Kunbin > > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to postmaster@genomichealth.com and delete this message, along > with any attachments, from your computer. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]