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.
Author
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)
#> $statistic
#> [1] 0.92
#>
#> $p_value
#> [1] 0.9216741
#>
#> $df
#> [1] 4
#>