gllm (version 0.38)

ld2: Estimate linkage disequilibrium between two codominant autosomal loci

Description

Fits a log-linear model for allelic association between two codominant autosomal loci. Measures of LD are odds ratios.

Usage

ld2(locus1, locus2)

Value

m0

base model

m1

estimating LD coefficient(s) assuming HWE

m2

testing HWE at locus 1

m3

testing HWE at locus 2

m4

estimating LD and HWD coefficient(s)

Arguments

locus1

is a character vector containing the genotypes at the first locus, or a RxC contingency table of genotype counts.

locus2

is a character vector containing the genotypes at the second locus.

Examples

MNS<-matrix(c(91,32,5,147,78,17,85,75,7), nr=3)
colnames(MNS)<-c("S/S","S/s","s/s")
rownames(MNS)<-c("M/M","M/N","N/N")
class(MNS)<-"table"
print(MNS)
res<-ld2(MNS)
print(res)