mutRate: Overall mutation rate

In magnusdv/pedmut: Mutation Models for Pedigree Likelihood Computations

Overall mutation rate

Description

Calculate the overall mutation rate at a locus, given a mutation model an a set of allele frequencies.

Usage

mutRate(mut, afreq = NULL)

Arguments

mut	A mutationModel() or mutationMatrix().
afreq	A vector of allele frequencies.

Details

The mutation rate is found by the formula 1 - sum(diag(mut) * afreq).

If mut is a mutationModel(), the rate is calculated separately for the male and female matrices.

Value

A single number, or (if mut is a mutationModel() and the female and male rates differ) a list of two numbers, named "female" and "male".

Examples

m = mutationMatrix("stepwise", alleles = 1:4, afreq = c(.1,.2,.3,.4),
                   rate = 0.01, rate2 = 1e-6, range = 0.1)
r = mutRate(m)

stopifnot(all.equal(r, 0.01))

magnusdv/pedmut documentation built on Jan. 31, 2024, 7:06 a.m.