LR: Likelihood ratios of pedigree hypotheses

In paramlink: Parametric Linkage and Other Pedigree Analysis in R

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 necessary 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

Author(s)

Magnus Dehli Vigeland and Thore Egeland

See Also

IBDtriangle, examineKinships

Examples

# 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)

paramlink documentation built on April 15, 2022, 9:06 a.m.