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RE: st: Hardy-Weinberg for multiallelic loci


From   "Doody, David R" <ddoody@fhcrc.org>
To   "'statalist@hsphsun2.harvard.edu'" <statalist@hsphsun2.harvard.edu>
Subject   RE: st: Hardy-Weinberg for multiallelic loci
Date   Mon, 14 Mar 2005 11:11:15 -0800

Thank you for the replies to my question.  To clarify, I'm looking to
calculate a p-value from the exact test, as I have some small cell counts.
It appears (from reading documentation) as though SAS will do this with the
PROC ALLELE command, but we don't have the SAS/GENETICS module, so I can't
confirm that.  I was hoping a similar command had been written in Stata, but
I may have to continue to cut and paste Stata output into other programs to
perform these tests.  No big deal...

Dave

-----Original Message-----
From: Cleves, Mario A [mailto:ClevesMarioA@uams.edu] 
Sent: Saturday, March 12, 2005 5:52 AM
To: statalist@hsphsun2.harvard.edu
Subject: RE: st: Hardy-Weinberg for multiallelic loci

David,

Neil is correct. -genhw- works for multiallelic loci. 
For multiallelic loci it performs an asymptotic test so it may not perform
well with sparse data. See Cleves M., Hardy-Weinberg equilibrium test &
allelle frequency estimation STB-48 sg110,3/99 (STB Reprints Vol 8, pages
280--284) for more details.

Make sure that you install the latest copy of the program from my website
"www.biostat-resources.com/stata".

Regards,
Mario.  

-----------------------------------------
Mario A. Cleves, Ph.D.
Associate Professor and Senior Biostatistician Department of Pediatrics UAMS
College of Medicine Arkansas Center for Birth Defects Research and
Prevention
11219 Financial Centre Parkway, Suite 250 Little Rock, AR  72211
Telephone: 501-364-5001
Fax: 501-364-5107
Email: ClevesMarioA@uams.edu
-----------------------------------------

-----Original Message-----
From: owner-statalist@hsphsun2.harvard.edu
[mailto:owner-statalist@hsphsun2.harvard.edu] On Behalf Of Neil Shephard
Sent: Saturday, March 12, 2005 6:48 AM
To: statalist@hsphsun2.harvard.edu; ddoody@fhcrc.org
Subject: Re: st: Hardy-Weinberg for multiallelic loci

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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