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README.md

umMDR

A unified model based MDR framework for detecting gene-gene interaction

Description

A two-step unified model based MDR approach (UM-MDR), in which, the significance of a multi-locus model, even a high-order model, can be easily obtained through a regression framework, and a semiparametric correction procedure is designed to control type I error rates

Installation

  • Download the package umMAD_0.1.tar.gz from this respository
  • To install, in R:
install.packages("path/umMDR_0.1.tar.gz", repos = NULL, type = "source")

Usage

umMDR(snp.all, phe, K = 2, cova = NULL, classm = "mean",
adj.main = "FALSE", nperm = 5)

Example

library(umMDR)
snps <- matrix(rbinom(100 * 5, 1, 0.2), nrow = 100)  ## generate 5 snps
phe <- rnorm(100)  ## generate phenotype
umMDR(snps, phe, 2)

More information about usage

library(umMDR)
help(umMDR)

Citation

Yu, Wenbao, Lee, Seungyeoun and Park, Taesung "A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions", Bioinformatics (2016) 32 (17): i605-i610.

Other Sources for the manuscript

gene_simu_nLD.R --- generate simulation data under 70 penetrance function and a 3-way interaction model

umMDR_simu.R --- run simulation Case1-case4

qqplot_simu.R --- generate qqplot in the manuscript

M_QMDR.R --- run MDR, QMDR or Multi-QMDR as a comparison