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st: New genetic analysis wrapper on SSC: -genass-

From   Neil Shephard <>
Subject   st: New genetic analysis wrapper on SSC: -genass-
Date   Tue, 18 Oct 2005 14:23:10 +0100

Dear all,

Thanks to Kit Baum a new command called -genass- is now available from SSC.

-genass- is a simple wrapper command for performing basic statistical
genetic analyses of case-control association studies.

Main features

* Calculation of genotype and allele frequencies in cases and controls.

* Testing for Hardy-Weinberg equilibrium in cases and controls.

* Genotypic and allelic tests of association.

* Tests of association under dominant and recessive disease models.

* Test of association for additive/multiplicative disease model.

* Calculation of pair-wise LD.

The main advantage of the command is that results are collated into a
Stata formatted data set which can then be loaded into memory and the
results viewed (either graphically using -graph- commands, or by using
the -list- command).

Additional Features

In addition to creating a Stata formatted data set, -genass- will (if
specified by the user), generate a series of graphs representing the
results, and/or generate a series of html formatted tables using Roger
Newson's -listtex- command.


As well as requiring Roger Newson's -listtex- command, this wrapper
also relies on the command -pwld- written by David Clayton.  This is
part of his -genassoc- package which can be downloaded and installed
from his site using the following series of commands...

. net from
. net install genassoc

-genass- is currently written for Stata 8.0


For a description of -genass- type...

. ssc describe genass

...and to install, type...

. ssc install genass

...followed by...

. help genass

This is my first attempt at writing a Stata program (one that I am
willing to release to a wider audience anyway), and I already have one
thing "To Do", however, all comments and feedback, along with
additions to this "To Do" list are more than welcome.



To Do

1. Make error messages more informative, so that reports are made as
to which marker is causing problem, and what that problem is.

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