clipp (version 1.1.1)

geno_freq_monogenic: 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)

Value

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

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.

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))