[BioC] Linkage Disequilibrium Analysis

[Stephanie M. Gogarten]

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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