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Ensemble of Filters: improve statistical power of gene-gene interaction filtering

• Description
  
  Using an ensemble approach to improve gene-gene interaction filtering results. Works for unstable filter (e.g. ReliefF and TuRF).
  
  
• Availability

  Note that only TuRF-E is able to significantly improve power in SNP interaction filtering. ReliefF-E is provided for evaluation purpose only. See [1] for more details.
  
  

  • TuRF-E.pl [download]
  • ReliefF-E.pl [download]
  • MDR.jar [download]
  (This is the mdr-2.0_beta_6.zip package. Please refer to the [authors site] for details.)
  • example dataset [download]

  The example dataset is obtained from study [2].

  * Perl v5, Java 5.0, and MDR 2.0 is required. Please place all program files in the same directory or you need to set Classpath for it to work.

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  Using TuRF-E.pl as example, to obtain the general information about the program, run following command in command line (without parameters):
  
  perl TuRF-E.pl

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  To test the program, run the program with the example dataset:
  
  perl TuRF-E.pl -f 20.400.1.txt

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  To report bugs, please email to following address:
  
  
  
  
• References

[1] Pengyi Yang, Joshua W.K. Ho, Albert Y. Zomaya, Bing B. Zhou, "Gene-gene interaction filtering with ensemble of filters", BMC Bioinformatics, 12:(Suppl 1):S10, 2011. [fulltext]
[2] Jason H. Moore et al., "Application of genetic algorithms to the discovery of complex models for simulation studies in human genetics", In: Proceedings of the Genetic and Evolutionary Computation Conference, 1150-1155, 2002. [fulltext]