SNPrank[1] is an eigenvector centrality algorithm that ranks the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN) [2]. Each SNP is ranked according to its overall contribution to the phenotype, including its main effect and second- and higher-order gene-gene interactions.
This software was created as a bioinformatics tool for usage by our research group, In Silico, as well as other researchers and interested parties.
jsnprank is developed and tested on 64-bit Linux (Ubuntu), but should work on any platform supported by Java (OpenJDK java version 1.6.0 tested).
jsnprank requires the jblas linear algebra library for matrix computations (tested with jblas version 1.1.1).
To compile the java classes:
javac -cp jblas-1.1.1.jar:. *.java
Once the Java source files have been compiled, you can run SNPrank from command-line:
java -cp jblas-1.1.1.jar:. snprank matrix.txt 0.85 output.txt
See AUTHORS file.
[1]N.A. Davis, J.E. Crowe, Jr., N.M. Pajewski, and B.A. McKinney. Surfing a genetic association interaction network to identify modulators of antibody response to smallpox vaccine. Genes and Immunity, 2010, doi: 10.1038/gene.2010.3. open access
[2]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