mdr: Perform a MDR.
In GeneticTools: Collection of Genetic Data Analysis Tools

Description Usage Arguments Details Value Author(s) References Examples

This function performs a Multifactor Dimension Reduction (MDR).

1	mdr(X,status,fold=2,t=NULL,cv=0,cvp=0.75,top=20,NAasValues=TRUE,fix=NULL)

`X`	Matrix with genotype information, see details.
`status`	Vector with group information of individuals in `X`.
`fold`	Maximum dimension of used contingency tables, see details.
`t`	Threshold for high/low risk.
`cv`	Amount of cross validation runs.
`cvp`	Ratio of cross-validation sample.
`top`	Length of each top list.
`NAasValues`	How shall NAs be treated.
`fix`	Shall one genotype be fixed.

The matrix X contains the genotype information or the filename of a ped/map filepair. If a ped/map filename is given the status information from this pair is taken and no further status object has to be given. In case status is given as well, we will take this information.

In case the matrix X is not given in 0,1,2 format the function recodeData recodes the data into the required 0,1,2 format.

The status vector is as long as X has individuals and specifies the group labels for each individual. Healthy individual shall be encoded as 0 and cases as 1. If the labeling is different we take the smaller values as controls and the larger one as cases.

The fold option specifies up to which dimension the contingency tables should be used. The current maximum is four.

The t option gives the threshold for the classification between high and low risk classes. The default is the ratio of the groups sizes.

An object of class mdr.

Daniel Fischer

Moore JH, Gilbert JC, Tsai CT, Chiang FT, Holden T, Barney N, White BC. (2006): A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol.2006 Jul 21;241(2):252-61.

# The datasets are not yet available. As soon as they will get published they will
# be also added to the package

## Not run: 
# Read in the genotype data
genotData <- read.table("MDR_data.txt",header=T)

# Extract the status information
status <- genotData[["Class"]]
genotData <- as.matrix(genotData[,-which((colnames(genotData)=="Class")==TRUE)])

# Bring the data into 0,1,2 format
temp <- recodeData(genotData)

# Perform the MDR
res <- mdr(X=temp,status=status,fold=3,top=20)

## End(Not run)