Hi All, I have a list of regions on the genome and I am looking  to find the list of SNPs in each region. Is there an R package that can help me to do that. Thanks for the Help [[alternative HTML version deleted]]

there are various approaches. the most immediately relevant packages are the SNPlocs.* packages from the annotation/metadata package set. if you do library(SNPlocs.Hsapiens.dbSNP.20071016) [a more recent image is available with a different name, last component beginning 2008], you can then do > c1 = getSNPlocs("chr1") > c1[1:10,] RefSNP_id alleles_as_ambig loc 1 4109793 K 115261 2 3926102 M 118514 3 3926103 Y 118548 4 3926104 K 118592 5 3926105 Y 118661 6 4081096 Y 161648 7 28855133 S 221411 8 28828438 K 221413 9 9730150 R 222312 10 3936964 Y 541148 some programming can be used to get indices of SNP for which loc lies in your regions On Thu, Jun 4, 2009 at 6:13 PM, Kay Jaja <kjaja27@yahoo.com> wrote: > Hi All, > > I have a list of regions on the genome and I am looking to find the list > of SNPs in each region. Is there an R package that can help me to do that. > > Thanks for the Help > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265 [[alternative HTML version deleted]]

keep the replies on the list. read the posting guide. what aspect of > biocLite("SNPlocs.Hsapiens.dbSNP.20071016") Running biocinstall version 2.3.13 with R version 2.8.0 Your version of R requires version 2.3 of Bioconductor. trying URL 'http://bioconductor.org/packages/2.3/data/annotation/bin/m acosx/universal/contrib/2.8/SNPlocs.Hsapiens.dbSNP.20071016_0.99.1.tgz ' Content type 'application/x-gzip' length 62173196 bytes (59.3 Mb) opened URL isn't working for you? please supply sessionInfo() result. On Fri, Jun 5, 2009 at 6:31 PM, Kay Jaja<kjaja27 at="" yahoo.com=""> wrote: > Hi, > > Thanks for the info but I tried to download the package and it says that it > is not available, am I missing somthing? > > thanks for your help > > ________________________________ > From: Vincent Carey <stvjc at="" channing.harvard.edu=""> > To: Kay Jaja <kjaja27 at="" yahoo.com=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Thursday, June 4, 2009 6:41:57 PM > Subject: Re: [BioC] extracting SNPs in a given region > > there are various approaches.? the most immediately relevant packages are > the > SNPlocs.* packages from the annotation/metadata package set. > > if you do library(SNPlocs.Hsapiens.dbSNP.20071016) [a more recent > image is available with a different name, last component beginning 2008], > you can then do > >> c1 = getSNPlocs("chr1") >> c1[1:10,] > ?? RefSNP_id alleles_as_ambig??? loc > 1??? 4109793??????????????? K 115261 > 2??? 3926102??????????????? M 118514 > 3??? 3926103??????????????? Y 118548 > 4??? 3926104??????????????? K 118592 > 5??? 3926105??????????????? Y 118661 > 6??? 4081096??????????????? Y 161648 > 7?? 28855133??????????????? S 221411 > 8?? 28828438??????????????? K 221413 > 9??? 9730150??????????????? R 222312 > 10?? 3936964??????????????? Y 541148 > > some programming can be used to get indices of SNP for which > loc lies in your regions > > On Thu, Jun 4, 2009 at 6:13 PM, Kay Jaja <kjaja27 at="" yahoo.com=""> wrote: >> >> Hi All, >> >> I have a list of regions on the genome and I am looking? to find the list >> of SNPs in each region. Is there an R package that can help me to do that. >> >> Thanks for the Help >> >> >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Vincent Carey, PhD > Biostatistics, Channing Lab > 617 525 2265 > > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265