Thanks Mete. I know about Haploview but I was hoping to find something in R. Thanks again. -Avoks On Thu, Jul 5, 2012 at 3:13 PM, Mete Civelek <mcivelek at="" mednet.ucla.edu=""> wrote: > Not sure about a Bioconductor package but you can try Haploview from Broad > Institute. > > -----Original Message----- > From: bioconductor-bounces at r-project.org > [mailto:bioconductor-bounces at r-project.org] On Behalf Of Ovokeraye > Achinike-Oduaran > Sent: Thursday, July 05, 2012 2:58 PM > To: bioconductor at r-project.org > Subject: [BioC] Linkage Disequilibrium Analysis > > Hi all, > > Is there a package that takes just SNPs rs IDs as input to perform LD > analysis and draw haplotype blocks? > > Thanks. > > -Avoks > > _______________________________________________ > 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 > > > IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

Or have a look at the functions getLD and getLDlarge from the trio package also available on CRAN, which can be used to compute LD values genome-wide. You can also plot the LD matrix, and estimate LD blocks using the function findLDblocks. These functions cannot only be applied to trio data, but were actually implemented for population- based data consisting of independent subjects (see the argument parentsOnly). Holger -------- Original-Nachricht -------- > Datum: Fri, 06 Jul 2012 07:34:28 -0700 > Von: "Stephanie M. Gogarten" <sdmorris at="" u.washington.edu=""> > An: Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> > CC: bioconductor at r-project.org > Betreff: Re: [BioC] Linkage Disequilibrium Analysis > GWASTools doesn't do LD, but I recommend SNPRelate, on CRAN. > > Stephanie > > > > > > Message: 5 > > Date: Thu, 05 Jul 2012 08:50:39 -0700 > > From: Valerie Obenchain<vobencha at="" fhcrc.org=""> > > To: Ovokeraye Achinike-Oduaran<ovokeraye at="" gmail.com=""> > > Cc:bioconductor at r-project.org > > Subject: Re: [BioC] Linkage Disequilibrium Analysis > > Message-ID:<4FF5B7CF.3050501 at fhcrc.org> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Have a look at the snpStats and GWASTools packages. > > > > Valerie > > > > > > On 07/05/2012 06:31 AM, Ovokeraye Achinike-Oduaran wrote: > >> >Thanks Mete. I know about Haploview but I was hoping to find something > in R. > >> > > >> >Thanks again. > >> > > >> >-Avoks > >> > > >> >On Thu, Jul 5, 2012 at 3:13 PM, Mete Civelek<mcivelek at="" mednet.ucla.edu=""> > wrote: > >>> >>Not sure about a Bioconductor package but you can try Haploview from > Broad > >>> >>Institute. > >>> >> > >>> >>-----Original Message----- > >>> >>From:bioconductor-bounces at r-project.org > >>> >>[mailto:bioconductor-bounces at r-project.org] On Behalf Of Ovokeraye > >>> >>Achinike-Oduaran > >>> >>Sent: Thursday, July 05, 2012 2:58 PM > >>> >>To:bioconductor at r-project.org > >>> >>Subject: [BioC] Linkage Disequilibrium Analysis > >>> >> > >>> >>Hi all, > >>> >> > >>> >>Is there a package that takes just SNPs rs IDs as input to perform > LD > >>> >>analysis and draw haplotype blocks? > >>> >> > >>> >>Thanks. > >>> >> > >>> >>-Avoks > >>> >> > >>> >>_______________________________________________ > >>> >>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 > >>> >> > >>> >> > >>> >>IMPORTANT WARNING: This email (and any attachments) is only > intended for the use of the person or entity to which it is addressed, and may > contain information that is privileged and confidential. You, the recipient, > are obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may subject > you to federal and state penalties. If you are not the intended recipient, > please immediately notify us by return email, and delete this message from > your computer. > >> >_______________________________________________ > >> >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.con ductor > > _______________________________________________ > 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

Thanks a bunch Stephanie, Vincent and Valerie. Kind regards, -Avoks On Fri, Jul 6, 2012 at 4:34 PM, Stephanie M. Gogarten <sdmorris at="" u.washington.edu=""> wrote: > GWASTools doesn't do LD, but I recommend SNPRelate, on CRAN. > > Stephanie > > >> >> Message: 5 >> Date: Thu, 05 Jul 2012 08:50:39 -0700 >> From: Valerie Obenchain<vobencha at="" fhcrc.org=""> >> To: Ovokeraye Achinike-Oduaran<ovokeraye at="" gmail.com=""> >> Cc:bioconductor at r-project.org >> Subject: Re: [BioC] Linkage Disequilibrium Analysis >> Message-ID:<4FF5B7CF.3050501 at fhcrc.org> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> >> Have a look at the snpStats and GWASTools packages. >> >> Valerie >> >> >> On 07/05/2012 06:31 AM, Ovokeraye Achinike-Oduaran wrote: >>> >>> >Thanks Mete. I know about Haploview but I was hoping to find something >>> > in R. >>> > >>> >Thanks again. >>> > >>> >-Avoks >>> > >>> >On Thu, Jul 5, 2012 at 3:13 PM, Mete Civelek<mcivelek at="" mednet.ucla.edu=""> >>> > wrote: >>>> >>>> >>Not sure about a Bioconductor package but you can try Haploview from >>>> >> Broad >>>> >>Institute. >>>> >> >>>> >>-----Original Message----- >>>> >>From:bioconductor-bounces at r-project.org >>>> >>[mailto:bioconductor-bounces at r-project.org] On Behalf Of Ovokeraye >>>> >>Achinike-Oduaran >>>> >>Sent: Thursday, July 05, 2012 2:58 PM >>>> >>To:bioconductor at r-project.org >>>> >>Subject: [BioC] Linkage Disequilibrium Analysis >>>> >> >>>> >>Hi all, >>>> >> >>>> >>Is there a package that takes just SNPs rs IDs as input to perform LD >>>> >>analysis and draw haplotype blocks? >>>> >> >>>> >>Thanks. >>>> >> >>>> >>-Avoks >>>> >> >>>> >>_______________________________________________ >>>> >>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 >>>> >> >>>> >> >>>> >>IMPORTANT WARNING: This email (and any attachments) is only intended >>>> >> for the use of the person or entity to which it is addressed, and may >>>> >> contain information that is privileged and confidential. You, the >>>> >> recipient, are obligated to maintain it in a safe, secure and confidential >>>> >> manner. Unauthorized redisclosure or failure to maintain confidentiality >>>> >> may subject you to federal and state penalties. If you are not the intended >>>> >> recipient, please immediately notify us by return email, and delete this >>>> >> message from your computer. >>> >>> >_______________________________________________ >>> >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 > >