Trial Enrichment

Overview

This package contains source code and brief instruction of the method use in the paper by Hu et al, titled "The benefits of using genetic information to design prevention trials", (2013) AJHG (in press)

Download

Please download this tar-ball archive

Requirement

• You will need to have R (>2.13), gnuplot (>4.2) and epstopdf software in order to run the package.
• This package has been developed and tested on Linux Ubuntu 12.10 and 12.04.2 LTS. While it should work on other Linux systems, they have not yet been tested.

Installation and Running

In order to run the software, you may run the following series of command

 tar xzvf trialEnrichment.v1.tar.gz
 cd trialEnrichment
 sh trialEnrichment.sh

Then you will see PDF files and other text outputs in results/ directory, which should be compatible to the published paper.

Modifying the software

• If you want to run the software in the exactly same setting to the paper, please change all the number of random samples from 1e5 (100K) to 1e6 (1M) in the code
• If you want to apply the method for different list of risk variables or different disease, you can modify the source code and provided data files.

License

Copyright (c) 2013, Hyun Min Kang <hmkang@umich.edu> and Youna Hu

Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.