expectedLR: Expected likelihood ratio In forrel: Forensic Pedigree Analysis and Relatedness Inference

 expectedLR R Documentation

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)
``````

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`.

Value

A positive number.

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. Ugly hack!
denomPed = nuclearPed(father = "fa", mother = "mo", nch = 1)
denomPed = addChildren(denomPed, father = "ch", mother = "mo", nch = 1)

# 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") = c(1, 1)
expectedLR(numPed, denomPed, ids = "ch", marker = m2)

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

``````

forrel documentation built on Nov. 19, 2023, 5:14 p.m.