GeneticTools (version 0.1)

mdr: Perform a MDR.

Description

This function performs a Multifactor Dimension Reduction.

Usage

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

Arguments

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.

Value

• An object of class mdr

Details

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.

References

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.

Examples

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

# Read in the genotype data
# genotData <- read.table("MDR_format_ready.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)