[BioC] Linkage Disequilibrium Analysis

[Ovokeraye Achinike-Oduaran]

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
>>>> >>
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>>>
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>