LRmutBounds: Pairwise LR bounds for proportional mutation models
In thoree/mut2: Reversible mutation matrices and pairwise likelihood ratios

LRmutBounds

R Documentation

Pairwise LR bounds for proportional mutation models

Description

Reversibility is assumed for the mutation model and the LR is calculated for a pair of non-inbred individuals comparing a kappa to unrelated.

Usage

LRmutBounds(p, kappa, K = 0, share = TRUE)

Arguments

`p`	Vector of real numbers. Allele frequency vector.
`kappa`	Vector of real numbers describing relationship. IBD parameters for 0,1,2 IBD alleles.
`K`	Real. Proportionality factor in proportional model
`share`	Logical. If TRUE, both are homozygous for the same allele, otherwise no akllele sharing.

Value

LR and the lower bound, assuming no allele sharing, and the upper bound assuming the individuals to be homozygous for the rarest allele.

Author(s)

Thore Egeland <Thore.Egeland@nmbu.no>

References

Egeland, Pinto and Amorim, FSI:Genetics (2017), \Sexpr[results=rd]{tools:::Rd_expr_doi("http://dx.doi.org/10.1016/j.fsigen.2017.04.018")}.

Examples


# Parent offspring relationship LR
p = c("1" = 0.2, "2" = 0.8)
M = mutationMatrix("proportional", afreq = p, rate = 0.003)
gamma = mut2::expectedMutationRate(M, p)
K = gamma/(1- sum(p^2))
kappa = c(0, 1, 0)
LRmutBounds(p, kappa, K, share = FALSE)
LRmutBounds(p, kappa, K, share = TRUE)

thoree/mut2 documentation built on May 16, 2023, 7:56 p.m.