make.contrasts: Calculate contrasts required by the function

In hwde: Models and Tests for Departure from Hardy-Weinberg Equilibrium and Independence Between Loci

Calculate contrasts required by the function

Description

Calculates the contrasts that hwde uses in fitting models for genotypic disequilibrium. At present these are limited to first order interaction terms between the distinct loci, possibly with distinct values foe each different level of a grouping factor.

Usage

make.contrasts(data = data[, loci], allele.chars = letters)

Arguments

data	Data frame, with one column per locus, and as many rows as there are observations. Genotypes are represented using a two-letter code, e.g., AA, Aa, aa
allele.chars	By default the letters "a", "b", ..., one for each locus, are used.

Details

Any pair of letters can be used for the two alleles. The setting of allele.chars determines the coding used in the model formulae. This function is called by hwde

Value

contrasts.df	Data frame whose columns hold the contrasts that will be explanatory variables for the Poisson regression model.
oset	Offset vector for the GLM model.
list.columns	List in which each element is a text string that holds the codes for a sequence of model terms.

Author(s)

J.H. Maindonald

See Also

identify.genotypes, called by make.contrasts

Examples

make.contrasts(data=c("AA","Aa","aa"))

hwde documentation built on Aug. 21, 2023, 9:07 a.m.