chisq_gl: Chi-Sq for GL

In segtest: Tests for Segregation Distortion in Polyploids

Chi-Sq for GL

Description

Calculates the MLE genotype and runs a chi-squared test assuming no double reduction and no preferential pairing.

Usage

chisq_gl(gl, g1, g2)

chisq_gl4(gl, g1, g2)

Arguments

gl	A matrix of offspring genotype log-likelihoods. The rows index the individuals and the columns index the possible genotypes. So gl[i, k] is the offspring genotype log-likelihood for individual i and genotype k-1.
g1	The first parent's genotype.
g2	The second parent's genotype.

Value

A list containing the chi-squared statistic, degrees of freedom, and p-value.

Functions

• chisq_gl4(): Alias for chisq_gl, for backwards compatibility.

Author(s)

Mira Thakkar and David Gerard

Examples

## null sim
set.seed(1)
g1 <- 2
g2 <- 2
gl <- simf1gl(n = 25, g1 = g1, g2 = g2, alpha = 0, xi2 = 1/3)
chisq_gl(gl = gl, g1 = g1, g2 = g2)

segtest documentation built on July 1, 2025, 1:07 a.m.