hwep (version 2.0.3)

zsegarray: Zygote segregation distributions.

Description

Obtains offspring genotype probabilities given parental probabilities, the ploidy of the species, and the overdispersion parameter, for all possible parental genotypes.

Usage

zsegarray(alpha, ploidy)

Value

An array of probabilities. Element (i, j, k) contains the probability of offspring dosage k-1 given parental dosages i-1 and j-1.

Arguments

alpha

A numeric vector containing the double reduction parameter(s). This should be a vector of length floor(ploidy/4) where alpha[i] is the probability of exactly i pairs of IBDR alleles being in the gamete. Note that sum(alpha) should be less than 1, as 1 - sum(alpha) is the probability of no double reduction.

ploidy

The ploidy of the species. This should be an even positive integer.

Author

David Gerard

Examples

ploidy <- 10
alpha <- c(0.5, 0.1)
p1 <- 4
p2 <- 3
segarray <- zsegarray(alpha = alpha, ploidy = ploidy)
graphics::plot(x = 0:10,
               y = segarray[p1 + 1, p2 + 1, ],
               type = "h",
               ylab = "Pr(dosage)",
               xlab = "dosage")
graphics::mtext(paste0("P1 dosage = ",
                       p1,
                       ", ",
                       "P2 dosage = ",
                       p2))