ld2: Estimate linkage disequilibrium between two codominant...

In gllm: Generalised log-Linear Model

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) 

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

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)

gllm documentation built on Oct. 18, 2022, 9:06 a.m.