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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

*

* For searches and help try:

* http://www.stata.com/support/faqs/res/findit.html

* http://www.stata.com/support/statalist/faq

* http://www.ats.ucla.edu/stat/stata/

-- 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 * * For searches and help try: * http://www.stata.com/support/faqs/res/findit.html * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/

**References**:**Re: re: st: genhw error***From:*n j cox <n.j.cox@durham.ac.uk>

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