gllm (version 0.38)

ld2.model: Write design and filter matrices for log-linear model of linkage disequilibrium between two codominant autosomal loci

Description

Write design and filter matrices for log-linear model of linkage disequilibrium between two codominant autosomal loci.

Usage

ld2.model(nall1, nall2, formula="~a1+a2+p1+p2+d")

Value

A list with components:

Geno

is a dummy contingency table showing the expected order.

s

is a vector of indices, one for each cell of the full (unobserved) contingency table, representing the appropriate cell of y

X

is the design matrix.

Arguments

nall1

is number of alleles at first codominant locus.

nall2

is number of alleles at first codominant locus.

formula

is character string listing terms to be included in model, where a1 denotes allele frequencies for locus 1, p1 the deviation from Hardy-Weinberg expectations for locus1, and d the intragametic allelic association parameters.