[BioC] Package for doing Copy number analsysi with LOH

[Stephanie M. Gogarten]

You might also try the GWASTools package.  See the section "chromosome 
anomaly detection" in the Data Cleaning vignette, and the "Preparing 
Affymetrix Data" vignette for how to format SNP 6.0 data for use with 
GWASTools.

Stephanie

On 5/30/12 3:00 AM, bioconductor-request at r-project.org wrote:
> Message: 16
> Date: Tue, 29 May 2012 10:04:07 -0700
> From: Valerie Obenchain<vobencha at fhcrc.org>
> To: Rajan Saini<drsaini22 at yahoo.com>
> Cc:"bioconductor at r-project.org"  <bioconductor at r-project.org>
> Subject: Re: [BioC] Package for doing Copy number analsysi with LOH
> Message-ID:<4FC50187.9080601 at fhcrc.org>
> Content-Type: text/plain
>
> A good place to start looking is the biocViews tree,
>
> http://bioconductor.org/packages/release/BiocViews.html#___Software
>
> These packages might be useful  cn.farms, cn.mops, genoset, SNPchip,
> snpStats, ...
>
> Valerie
>
>
> On 05/17/2012 06:39 PM, Rajan Saini wrote:
>> >  Dear Bioconductor community,
>> >
>> >       I am looking for a package that does Copy number along with LOH analysis (B allele frequency) for intensity files from SNP 6.0 arrays. Please direct me to the right package for this kind of analysis. Thank you very much in advance
>> >
>> >
>> >  Raj
>> >  	[[alternative HTML version deleted]]
>> >
>> >
>> >
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