impute.mdr {imputeMDR} | R Documentation |
This function provides various approaches to handling missing values for the MDR analysis of incomplete data to identify gene-gene interactions using biallelic marker data in genetic association studies
impute.mdr(dataset, colresp, cs, combi, cv.fold = 10, na.method = 0, max_iter = 30, randomize = FALSE)
dataset |
A matrix of SNP data with class variable (response; phenotype; disease status). Genotypes must be coded as allele counts (0,1,2). Missing genotypes should be coded as 3 |
colresp |
Column number of class variables in the dataset. No missing value is allowed for the class variable |
cs |
The value used to indicate "case (affected)" for class variable |
combi |
The number of SNPs considered simultaneously as predictor variables (An order of interactions to analyze) |
cv.fold |
The number of folds k for k-fold cross-validation |
na.method |
Options for missing handling approaches. na.method = 0 for complete data, na.method = 1 for treating missing genotypes as another genotype category, na.method=2 for using available data for given number of SNPs under consideration as a model, na.method=3 for using method of imputing missing information by using EM (expectation-maximization) algorithm |
max_iter |
The number of maximum iteration in EM impute approach (na.method=3). In order to apply one-step EM approach, set this argument as 1 |
randomize |
Logical. If 'TRUE' the cross validation sets are randomized |
min.comb |
Marker combinations with the minimum error rate in each cross validation |
train.erate |
Training errors for selected marker combination |
test.erate |
Test error of the selected marker combination |
best.combi |
The best combination that was selected most frequently across k-fold cross validation |
Junghyun Namkung, Taeyoung Hwang, MinSeok Kwon, Sunggon Yi and Wonil Chung
Maintainer: Junghyun Namkung <jh.namkung@gmail.com>
Namkung J, Elston RC, Yang JM, Park T. "Identification of gene-gene interactions in the presence of missing data using the multifactor dimensionality reduction method" Genet Epidemiol. 2009 Nov;33(7):646-56.
## sample data with missing values data(incomplete) ## analysis example of 2nd order gene-gene interaction test impute.mdr(incomplete, colresp=1, cs=1, combi=2, cv.fold = 10,na.method=2)