geno_freq_monogenic: Calculate genotype frequencies from allele frequencies using...

In clipp: Calculating Likelihoods by Pedigree Paring

Calculate genotype frequencies from allele frequencies using Hardy-Weinberg equilibrium

Description

A function to calculate the unphased genotype frequencies for a single autosomal genetic locus that has given allele frequencies and is at Hardy-Weinberg equilibrium (HWE).

Usage

geno_freq_monogenic(p_alleles, annotate = FALSE)

Arguments

p_alleles	A vector of strictly positive numbers that sum to 1, with p_alleles[i] interpreted as the allele frequency of the ith allele of the genetic locus. When annotate is TRUE, the names of the alleles will be taken to be names(p_alleles) or, if names(p_alleles) is NULL, to be 1:length(p_alleles).
annotate	A logical flag. When FALSE (the default), the function returns a vector suitable to be used as the geno_freq argument of pedigree_loglikelihood. When TRUE, the function adds a names attribute to this vector to indicate which genotype corresponds to which element.

Details

For a genetic locus at Hardy-Weinberg equilibrium, the population allele frequencies at the locus determine the population genotype frequencies; see Sections 1.2 and 1.3 of (Lange, 2002). Given a vector p_alleles containing the allele frequencies, this function returns the frequencies of the possible unphased genotypes, in a particular order that can be viewed by setting annotate to TRUE. If the alleles are named 1:length(p_alleles), so that p_alleles[i] is the frequency of allele i, then the unphased genotypes are named 1/1, 1/2, .... Note that if the output of this function is to be used as the geno_freq argument of pedigree_loglikelihood then the annotate option must be set to FALSE.

Value

A vector of strictly positive numbers (the genotype frequencies) that sum to 1, named with the genotype names if annotate is TRUE.

References

Lange K. Mathematical and Statistical Methods for Genetic Analysis (second edition). Springer, New York. 2002.

Examples

# Genotype frequencies for a biallelic locus at HWE and with a minor allele frequency of 10%
p_alleles <- c(0.9, 0.1)
geno_freq_monogenic(p_alleles, annotate = TRUE)

# Genotype frequencies for a triallelic locus at Hardy-Weinberg equilibrium
p_alleles <- c(0.85, 0.1, 0.05)
geno_freq_monogenic(p_alleles, annotate = TRUE)
sum(geno_freq_monogenic(p_alleles))

clipp documentation built on July 12, 2022, 9:05 a.m.