GAIN[1] 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.
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.
[1]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