hwefreq: Generate HWE genotype frequencies

In hwep: Hardy-Weinberg Equilibrium in Polyploids

Generate HWE genotype frequencies

Description

Generate genotype frequencies under Hardy-Weinberg equilibrium given the allele frequency of the reference allele (r), the double reduction parameter (alpha), and the ploidy of the species (ploidy).

Usage

hwefreq(
  r,
  alpha,
  ploidy,
  niter = 100,
  tol = sqrt(.Machine$double.eps),
  more = FALSE
)

Arguments

r	The allele frequency of the reference allele.
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.
niter	The maximum number of iterations to simulate.
tol	The stopping criterion on the Chi-square divergence between old and new genotype frequencies.
more	A logical. Should we return more output (TRUE) or less (FALSE). See the Value section for details.

Details

If alpha is not all 0, then this function repeatedly applies freqnext() to simulate genotype frequencies under HWE. Otherwise, it uses dbinom().

Value

If more = FALSE, then returns just the genotype frequencies after niter generations of random mating. If more = TRUE, then returns a list with these genotype frequencies, as well as the parental gamete frequencies.

Author(s)

David Gerard

Examples

freq1 <- hwefreq(r = 0.5, alpha = 0, ploidy = 4)
freq2 <- hwefreq(r = 0.5, alpha = 1/6, ploidy = 4)

plot(x = 0:4,
     y = freq1,
     type = "h",
     ylim = c(0, 0.4),
     xlab = "dosage",
     ylab = "Pr(dosage)")
plot(x = 0:4,
     y = freq2,
     type = "h",
     ylim = c(0, 0.4),
     xlab = "dosage",
     ylab = "Pr(dosage)")

hwep documentation built on May 31, 2023, 9:06 p.m.