Fuzzy set based approach to generalized multi-factor dimensionality reduction analysis of gene-gene interactions (FGMDR)

Introduction

This method is fuzzy generalized multifactor dimensionality reduction (FGMDR) method as an extension of GMDR method to detect gene-gene interactions associated with disease using fuzzy set theory. Details of Fuzzy MDR is explained in the following paper. More details of FGMDR will be updated as soon as published.

Citation

Jung, H.-Y., et al. (2016) A novel fuzzy set based multifactor dimensionality reduction method for detecting gene-gene interaction, Computational Biology and Chemistry.

Example

#glm fitting for residual calculation with equation as class~covariates form
fit_model <- glm(temp_data[,n]~temp_data[,n-1], data= temp_data, family = binomial(link = "logit")) 

#standard residuals for FGMDR
temp_data$res<-residuals(fit_model, type="response")

#data transformation, SNPs(9:24) and residuals(8)
data_FGMDR <- temp_data[,c(9:24, 8)]

#run FGMDR with 2-locus, 0.5 threshold and 10-fold cross validation
res_2_2<-FGMDR(data_FGMDR, 2, 0.5, 10)

#drawing result figure
plot_FMDR(res_2,2)

Download

The above R code be download from the below link.
Download