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MDR (version 1.2)

MDR-package: Detect gene-gene interactions using multifactor dimensionality reduction

Description

Performs multifactor dimensionality reduction (MDR) to detect potential gene-gene interactions in case-control studies, using balanced accuracy as an evaluation measure to rank potential models. Offers both cross-validation (CV) and a three-way split as internal validation methods to prevent over-fitting, as well as permutation testing and post-hoc prediction estimates.

Arguments

Index

  • mdr Performs MDR over a specified set of combinations of variables/loci
  • mdr.hr Estimates the accuracy of an MDR model given high-risk/low-risk status
  • mdr.cv Implements MDR with cross-validation
  • mdr.3WS Implements MDR with a three-way split internal model validation
  • boot.error Calculates a post-hoc bootstrap prediction estimate of classification error
  • mdr.ca.adj Calculates a post-hoc adjusted prediction estimate of classification accuracy
  • permute.mdr Performs a permutation test on an object of class mdr
  • plot Plots the best model of an object of class mdr
  • summary Summarizes a previously fit object of class mdr
  • predict Predicts case-control status on new data using a previously fit object of class mdr

Details

Package:
MDR
Type:
Package
Version:
1.1
Date:
2011-07-16
License:
GPL-2
LazyLoad:
yes
~~ This is an early test release. ~~

References

Ritchie MD et al (2001). Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hm Genet 69(1): 138-147.

Hahn LW, Ritchie MD, Moore JH (2003). Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19(3):376-82.

Velez DR et al (2007). A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol 31(4): 306-315.

Winham SJ and Motsinger AA (2010). The effect of retrospective sampling on estimates of prediction error for multifactor dimensionality reduction. Annals of Human Genetics.

Winham SJ and Motsinger AA (2010). A comparison of internal validation techniques for multifactor dimensionality reduction. BMC Bioinformatics.

Edwards TL et al (2010). A General Framework for Formal Tests of Interaction after Exhaustive Search Methods with Applications to MDR and MDR-PDT. PLoS One 5(2).