LD-EM: Estimating LD using EM algorithm

In YQHuFD/SLIDE: Nonparametric and Inheritance Model-free Test for Association with Multiple Loci in the Retrospective Case-control Study

Description

This function is to estimate pairwise linkage disequilibrium with EM algorithm.

Usage

ld.em(genotype)

Arguments

genotype

numeric matrix or data frame with genotype data coded as 0, 1, 2. No missing data is allowed.

Details

There is no missing data.

Value

The list contains the LD matrix, D' matrix and r^2 matrix.

Author(s)

Chan Wang and Yue-Qing Hu

References

Chan Wang, Shufang Deng, Leiming Sun, Liming Li and Yue-Qing Hu, Nonparametric and Inheritance Model-free Test for Association with Multiple Loci in the Retrospective Case-control Study

Examples

genotype<-matrix(sample(c(0,1,2),5000,replace=TRUE),500,10) ### 500 individuals and 10 SNPs

LD<-ld.em(genotype)

LD_orignal<-LD[[1]]

LD_D<-LD[[2]]

LD_r<-LD[[3]]

YQHuFD/SLIDE documentation built on May 23, 2019, 1:09 p.m.