Python implementation of GAIN
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README.md

pygain

Genetic Association Interaction Network (GAIN) tool

Description

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.

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)

Contributors

See AUTHORS file.

References

[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