[BioC] Linkage Disequilibrium Analysis

[Holger Schwender]

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
> >>> >>
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