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Re: st: genhw error


From   David Airey <david.airey@Vanderbilt.Edu>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: genhw error
Date   Tue, 23 Oct 2007 14:17:48 -0500

.

hwsnp is also by the Mario Cleves' and allows testing of multiple snps at once.

There is also David Clayton's fantastic set of programs for genetic analysis in Stata. HWE is tested by one of those as well, and there is helpful documentation on manipulating data so that each row is a person (genotype models) or each row is a chromosome (allele counting models); the latter assume HWE.

http://www-gene.cimr.cam.ac.uk/clayton/software/stata/

On Oct 23, 2007, at 2:08 PM, n j cox wrote:


Tony and David's experiences can be reconciled. Tony is
using an old -genhw-. It is expecting three numbers,
the frequencies of different phenotypes [? I'm a geographer],
and is only given two, and it chokes on a comma where
it expects to see a number. This is because Tony's data
is 4 AA, 2 AG -- and, importantly, 0 GG, except that last
frequency is not being passed to -genhwi-. Evidently this was
an old bug in -genhw- that was caught and fixed. Thus
Tony should update by using -findit- to find the latest
version on Mario Cleves' website.

Nick
n.j.cox@durham.ac.uk

David Airey

I am not seeing the same problem with genhw. I'm Stata MP OS X.

. which genhw
/Users/dairey/Library/Application Support/Stata/ado/plus/g/genhw.ado
*! version 7.0.0 14mar2005

Tony Black

I am having difficulty with the "genhw" command
With this simple dataset:

allele1 allele2
A A
A G
A A
A G
A A
A A

I issue the following command:

. genhw allele1 allele2

and get this result (in red)

',' found where integer expected

I set trace on and it seems to be blowing up in "genhwi" -- here is a snip
from the trace file

- genhwi `vars', `labopt' `binvar'
= genhwi 4 2, label(AA AG)

---------------------------------------------------------------------- ------
------------------- begin genhwi ---
- version 6
- qui {
- gettoken AA 0 : 0, parse(" ,")
- gettoken Aa 0 : 0, parse(" ,")
- gettoken aa 0 : 0, parse(" ,")
- confirm integer number `AA'
= confirm integer number 4
- confirm integer number `Aa'
= confirm integer number 2
- confirm integer number `aa'
= confirm integer number ,
',' found where integer expected


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--
David C. Airey, Ph.D.
Pharmacology Research Assistant Professor
Center for Human Genetics Research Member

Department of Pharmacology
School of Medicine
Vanderbilt University
Rm 8158A Bldg MR3
465 21st Avenue South
Nashville, TN 37232-8548

TEL   (615) 936-1510
FAX   (615) 936-3747
EMAIL david.airey@vanderbilt.edu
URL   http://people.vanderbilt.edu/~david.c.airey/dca_cv.pdf
URL   http://www.vanderbilt.edu/pharmacology


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