SPADIS is an algorithm designed to recover single nucleotide polymorphisms (SNPs) that are related with a phenotype in genome wide association studies (GWAS) using a SNP-SNP interaction network.
SPADIS provides a MATLAB interface for ease of use. These instructions will guide you to build and run SPADIS on MATLAB.
Building SPADIS requires the Boost C++ library. Most Linux distributions come with Boost pre-installed. However, if your operating system does not include Boost, follow the Boost getting started guide for instructions on how to install it.
Check Boost website for more information.
In order to build SPADIS for MATLAB, you can use GNU make:
make matlab
or directly run the MATLAB script for building mex files:
build_mex.m
We provide a few examples on how to run SPADIS on MATLAB. Simply run the demo file:
demo.m
In the provided examples, the genotype and flowering time phenotypes data of Arabidopsis Thaliana (AT) obtained from Atwell et. al. (2010) are used. For descriptions and format of the data, check the readme file for data.
This project is licensed under GNU GPL v3 - see the LICENSE file for details.
Yilmaz, Serhan, Tastan, Oznur & Cicek, A. Ercument (2018). SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS. bioRxiv
Atwell, S. et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature, 465(7298), 627–631.
Wu, M. C. et al. (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. The American Journal of Human Genetics, 89(1), 82–93.