[BioC] GWASTools for analyzing Canine_HD genotyping data

[Stephanie M. Gogarten]

Dear Tendai,

The "GWAS Data Cleaning" vignette that comes with GWASTools shows how to 
import plain text files (we usually start with the FinalReport files 
output from Illumina's GenomeStudio) into the NetCDF format used by 
GWASTools.  You will need to define integer chromosome codes for 
autosomes and sex chromosomes, and then specify these codes when you 
create objects in GWASTools throughout your analysis (since the default 
is human with 22 autosomes).

You will need the development version of GWASTools (1.5.4 or later), 
which has support for different numbers of autosomes.  It can be found 
here: http://www.bioconductor.org/packages/devel/bioc/html/GWASTools.html

In the documentation for the GenotypeData class ("?GenotypeData"), there 
is an example of how to set up GWASTools with a non-human organism.

I am copying the Bioconductor mailing list.  Please include 
bioconductor at r-project.org if you have any follow-up questions, for the 
benefit of other package users.

Stephanie

On 2/25/13 10:57 AM, Mutangadura, Tendai wrote:
> Thanks.
>
> -tendai
>
> *From:*Xiuwen Zheng [mailto:zhengx at u.washington.edu]
> *Sent:* Monday, February 25, 2013 12:55 PM
> *To:* Mutangadura, Tendai
> *Cc:* Stephanie M. Gogarten
> *Subject:* Re: GWASTools for analyzing Canine_HD genotyping data
>
> Hi Tendai,
>
> I am forwarding your email to Stephanie M. Gogarten, who developed and
> maintain the GWASTools package.
>
> Best,
>
> Xiuwen
>
> On Feb 25, 2013, at 10:42 AM, "Mutangadura, Tendai" <tendai at missouri.edu
> <mailto:tendai at missouri.edu>> wrote:
>
>
>
> Dr. Zheng,
>
> Does the Bioconductor GWASTools work with the Illumina Canine_HD chip?
> We use this chip for genotyping our research dogs. If so, are there
> examples on the web on how to use the software package with the Infinium
> canine_HD chip? I have seen examples online for analyzing what looks
> like Affymetrix sample data, and I do not know how to relate this to the
> canine context.
> Thanks,
> -tendai
>