GWASTools for analyzing Canine_HD genotyping data
Entering edit mode
Last seen 11 weeks ago
University of Washington
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: 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 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] > *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=""""> <mailto:tendai at="""">> 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 >
Organism cdf GWASTools Organism cdf GWASTools • 852 views
Entering edit mode

Even if your data only contains autosomes, be sure to set chromosome codes for X, Y, XY, and M to numbers >38. Otherwise the default codes for these chromosomes will remain as 23-26 and your autosomes will not be interpreted correctly.


Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 141 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.4