hwep (version 2.0.3)

hwefreq: 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
)

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.

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.

Author

David Gerard

Details

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

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)")