log_likelihood_diploid: calculate the log likelihood of observing diploid ancestry...

In thijsjanzen/junctions: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages

calculate the log likelihood of observing diploid ancestry data.

Description

Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture

Usage

log_likelihood_diploid(
  local_anc_matrix,
  pop_size,
  freq_ancestor_1 = 0.5,
  t,
  phased = FALSE,
  num_threads = 1
)

Arguments

local_anc_matrix	a matrix with four columns: column 1) chromosome indicator, 2) location of marker in Morgan on respective chromosome 3) ancestry at chromosome 4) ancestry at chromosome 2.
pop_size	population size
freq_ancestor_1	Frequency of ancestor 1 at t = 0
t	time since admixture
phased	is the data phased or not? default is false.
num_threads	number of threads, default is one thread. Set to -1 to use all available threads.

Value

log likelihood

thijsjanzen/junctions documentation built on June 11, 2025, 11:36 p.m.