Detection-of-epistasis-patterns-in-genetic-data.

Master2 project Bioinformatics, University of Nantes By Quentin Clayssen, Antoine Laine

Detection of epistasis patterns using Memetic algorithm and Path Relinking method

Initialisation of project

In order to compile the whole project a makefile is provided at project's root. This makefile will call each method's makefile and produce both executables. This makefile, can recreate directory structure if needed.

Compilation instruction

To recreate directory structure for both methods, please call this line at the root of the project:

make install

To compile both methods, please call this lines at the root of the project:

make

If a recompilation is needed please use to purge all compiled files:

make clean

Generate a naive data set

This project is provided with a tool to generate some naive data set. This tool fit with a logistic regression and produce a data set of given sizes with a given number of causal SNPs. This operation is performed by simu_naive.py.

./simu_naive.py -p simu_naive -f 1 -v 28 -pa 2000 -o toy_dataset -c 2000 -s 2