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


From   Neil Shephard <nshephard@gmail.com>
To   statalist@hsphsun2.harvard.edu
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.

Dependencies
--------------

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

-genass- is currently written for Stata 8.0

Installation
--------------

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.

Regards

Neil

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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