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Re: st: Hardy-Weinberg for multiallelic loci


From   Neil Shephard <nshephard@gmail.com>
To   statalist@hsphsun2.harvard.edu, ddoody@fhcrc.org
Subject   Re: st: Hardy-Weinberg for multiallelic loci
Date   Sat, 12 Mar 2005 12:47:32 +0000

On Fri, 11 Mar 2005 15:54:39 -0800, Doody, David R <ddoody@fhcrc.org> wrote:
>  
> I searched the archives for an answer to this question, but was
> unsuccessful.  Sorry if it's been discussed before.  I'm trying to test my
> case-control data to confirm they're in Hardy-Weinberg equilibrium.  I can
> use genhw for SNPs, but I have a few multiallelic loci.  I've seen various
> other packages which seem to use a method proposed by Guo and Thompson
> (using Markov chain methods?), but they require extra effort to get the data
> into a format for those packages to work.  I'm wondering if anyone has
> developed programs for this method within Stata?  Or is there another method
> which is preferred for testing HWE for multiallelic loci that I should know
> about?  Thanks in advance. 
>   
 The -genhw- command will work with multi-allelic loci (see the help
page for details of format).  You don't explicitly state the format
your data is in, but I suspect it may already fit the required format
(i.e. two variables for each locus, with the alleles an individual
carries listed in each variable).

The reported statistic is simply the Pearson Chi^2 for the observed
and expected genotyped frequencies.

HTH's

Neil
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