// GWiS: a gene-based test of association
// Copyright (C) 2011 Hailiang Huang, Pritam Chanda, Joel S. Bader and Dan E. Arking
// contact: email@example.com
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
// You should have received a copy of the GNU General Public License along
// with this program; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
GNU Scientific Library (GSL) is required to compile and use GWiS (http://www.gnu.org/software/gsl/).
Type "make" to compile and link. "GWiS" is the final execuable.
GWiS will read the inputs from ./sample and write the outputs to ./result.
Will generate a sample input for 20 indepedent SNPs and 8000
individuals. The generated files will be at ./sample.
plink is required (http://pngu.mgh.harvard.edu/~purcell/plink/)
./GWiS working_dir chr trait destination_dir random_seed
--working_dir: dir having the trait and the genotype files
--chr: such as chr1, chr2 ...
--trait: GWiS will look for "trait.tfam" in the working directory
--destination_dir: destination for your output files
--random_seed: random seed
GWiS by default runs up to 1 million permutations and outputs results for GWiS, minSNP, minSNP-P and BIMBAM. It is possible to change the these parameters by setting the GWiS environment variables. An example to set the environment variable 'VAR' in the bash shell is
1) set the maximum number of permutations
2) skip/restore GWiS permutations (GWiS model will still be estimated)
3) skip/restore minSNP
4) skip/restore minSNP-P
5) skip/restore BIMBAM
having the test statistics of each SNP in the study
mapping from SNPs to genes
having the results from minSNP method
having the results from minSNP-P method
having the results from BimBam method
having the results from GWiS model selection
having the results from GWiS permutations