A function to calculate the likelihood ratio

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Description

This function calculates the likelihood ratio for an allele causing a disease asssuming that the allele is extremely rare so that all family members who have the allele got it directly from a common ancestor in the pedigree.

Usage

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calculate.likelihood.ratio(ped, affected.boolean)

Arguments

ped

A dataframe of a pedigree containing id, momid, dadid, age(Current age or age affected), y.born(year born), female(a logical where 1 is female and 0 is male), and genotype(0 is non-carrier, 1 carrier, and 2 unknown) in any order but with these specific column names.

affected.boolean

A boolean(or logical) vector where 0 is unaffected and 1 is affected.

Value

likelihood.ratio

The resultant likelihood ratio

separating.meioses

The number of meioses separating all individuals known to have the genotype including those that are are indirectly known to have the genotype.

number.genotypes.found

The number of permissible genotypes found for the pedigree.

Author(s)

John Michael O. Ranola and Brian H. Shirts

Examples

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##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.