Estimate linkage disequilibrium between two codominant autosomal loci

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Description

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

Usage

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ld2(locus1, locus2) 

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.

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)

Examples

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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)