Genetic Association Interaction Network (GAIN) tool
GAIN is based on interaction information between three attributes; in this case, between two single nucleotide polymporphisms (SNPs) and a class or phenotype attribute. Interaction information is the gain in phenotype information obtained by considering SNP A and SNP B jointly beyond the phenotype information that would be gained by considering SNPs A and B independently.
This software was created as a bioinformatics tool for usage by our research group, In Silico, as well as other researchers and interested parties.
Dependencies and Usage
pygain is developed and tested on 64-bit Linux (Ubuntu), but should work on any platform supported by Python (Python version 2.6.5 tested).
To run pysnprank from command-line:
./gain.py -i plink-data.raw -o gain-matrix.txt
Additional parameters: Usage: gain.py [OPTIONS]
Construct GAIN matrix from PLINK .raw or tab-delimited file Options: --version display program version --help -h display this help and exit --input -i Input file (default: stdin) --filter Filter to exclude SNPs listed in file --export-sif -e Export Cytoscape .sif file --output -o Output file (default: stdout)
See AUTHORS file.
B.A. McKinney, J.Guo, J.E. Crowe, Jr., and D. Tian. Capturing the spectrum of interaction effects in genetic association studies by simulated evaporative cooling network analysis. PLoS Genetics 2009, 5(3): e1000432. doi:10.1371/journal.pgen.1000432. open access