MDR-package: Detect gene-gene interactions using multifactor...

In MDR: 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.

Details

Package:	MDR
Type:	Package
Version:	1.1
Date:	2011-07-16
License:	GPL-2
LazyLoad:	yes

~~ This is an early test release. ~~

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

Author(s)

Stacey Winham

Maintainers: Stacey Winham <[e-mail]>

Alison Motsinger-Reif <[e-mail]>

David Reif <[e-mail]>

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).

MDR documentation built on May 29, 2017, 7:05 p.m.