paramlink (version 1.1-2)

LR: Likelihood ratios of pedigree hypotheses

Description

This function computes likelihood ratios for a given a list of pedigrees (linkdat/singletons objects), one of which is the 'reference', with genotype data from the same set of markers. Data exported from the 'Familias' software can be analysed by using Familias2linkdat prior to calling this function.

Usage

LR(x, ref, markers)

Arguments

x

A list of pedigrees. Each pedigree is either a single linkdat/singleton object, or a list of such objects (the latter is neccessary if the pedigree is disconnected).

ref

A single integer, indicating the index of the reference pedigree. This is used in the denominator of each LR.

markers

A vector of integers, indexing which markers should be included. If NULL (the default) all markers are used.

Value

A list with entries

LR

Likelihood ratios

LRperMarker

Likelihood ratios for each marker

likelihoodsPerSystem

Likelihoods for each marker

time

user, system and elapsed time

See Also

IBDtriangle, examineKinships

Examples

# NOT RUN {
# Simulate genotypes for 5 tetraallelic markers for a pair of full sibs
set.seed(123)
sibs = simpleSim(nuclearPed(2), N=5, alleles=1:4, available=3:4)

# Create two alternative hypotheses and transfer the simulated genotypes to them
halfsibs = addOffspring(nuclearPed(1),father=1,noffs=1,id=4)
halfsibs = transferMarkerdata(sibs, halfsibs)

unrel = list(singleton(3), singleton(4))
unrel = transferMarkerdata(sibs, unrel)

# Compute LR with 'unrelated' as reference
LR(list(sibs, halfsibs, unrel), ref=3)

# }
# NOT RUN {
data(adoption)
x = Familias2linkdat(adoption$pedigrees, adoption$datamatrix, adoption$loci)
result = LRparamlink(x, ref=2)
result33 = LRparamlink(x, ref=2, marker=c(11,33))
# }
# NOT RUN {
# }