like_glpknown_3: Likelihood under three parameter model when using offspring...

In segtest: Tests for Segregation Distortion in Polyploids

Likelihood under three parameter model when using offspring genotypes likelihoods but parent genotypes are known.

Description

This is under the three parameter model.

Usage

like_glpknown_3(gl, tau, beta, gamma1, gamma2, g1, g2, log_p = TRUE)

Arguments

gl	The matrix of genotype likelihoods of the offspring. Rows index The individuals, columns index the genotypes.
tau	The probability of quadrivalent formation.
beta	The probability of double reduction given quadrivalent formation.
gamma1	The probability of AA_aa pairing for parent 1.
gamma2	The probability of AA_aa pairing for parent 2.
g1	Parent 1's genotype.
g2	Parent 2's genotype.
log_p	A logical. Should we return the log likelihood or not?

Value

The (log) likelihood of the three parameter model when using genotype likelihoods.

Author(s)

David Gerard

Examples

g1 <- 1
g2 <- 0
gl <- simf1gl(
  n = 25,
  g1 = g1,
  g2 = g2,
  rd = 10,
  alpha = 0,
  xi1 = 1/3,
  xi2 = 1/3)
like_glpknown_3(
  gl = gl,
  tau = 1/2,
  beta = 1/12,
  gamma1 = 1/3,
  gamma2 = 1/3,
  g1 = g1,
  g2 = g2,
  log_p = TRUE)

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