forrel (version 1.7.1)

expectedLR: Expected likelihood ratio

Description

This function computes the expected LR for a single marker, in a kinship test comparing two hypothesised relationships between a set of individuals. The true relationship may differ from both hypotheses. Some individuals may already be genotyped, while others are available for typing. The implementation uses oneMarkerDistribution() to find the joint genotype distribution for the available individuals, conditional on the known data, in each pedigree.

Usage

expectedLR(numeratorPed, denominatorPed, truePed = numeratorPed, ids, marker)

Value

A positive number.

Arguments

numeratorPed

A ped object.

denominatorPed

A ped object.

truePed

A ped object.

ids

A vector of ID labels corresponding to untyped pedigree members. (These must be members of all three input pedigrees).

marker

either a marker object compatible with numeratorPed, or the name or index of a marker attached to numeratorPed.

Examples

#---------
# Curious example showing that ELR may decrease
# by typing additional reference individuals
#---------

# Numerator ped
numPed = nuclearPed(father = "fa", mother = "mo", child = "ch")

# Denominator ped: fa, mo, ch are unrelated. (Hack!)
denomPed = halfSibPed() |> relabel(old = 1:3, new = c("mo", "fa", "ch"))

# Scenario 1: Only mother is typed; genotype 1/2
p = 0.9
m1 = marker(numPed, mo = "1/2", afreq = c("1" = p, "2" = 1-p))
expectedLR(numPed, denomPed, ids = "ch", marker = m1)

1/(8*p*(1-p)) + 1/2 # exact formula

# Scenario 2: Include father, with genotype 1/1
m2 = m1
genotype(m2, id = "fa") = "1/1"
expectedLR(numPed, denomPed, ids = "ch", marker = m2)

1/(8*p*(1-p)) + 1/(4*p^2) # exact formula