Instructions for running models described In:
"Analysis of Single-Locus Tests to Detect Gene/Disease Associations" by Roeder, Bacanu, Sonpar, Zhang, and Devlin.
tmax.R is a program for performing association analysis on a set of linked loci within a targeted region. It has 2 optional approaches, TMAX and SMAX, which are based on single locus test statistics (the log odds ratio) computed for each measured locus. TMAX utilizes the maximum of this series of test statistics, correcting for multiple testing by permutation of case-control status. SMAX utilizes the maximum of a smoothed curve fitted to the series of of test statistics. Again, the p-value is determined by permutation of case-control status.
The system on which the program is run has to have R (http://www.r-project.org) installed on it. Thus, the first step in running the program will be to download a copy of R, if you do not already have them installed. To download R, go to http://www.r-project.org and follow the necessary links to download R.