mix3Familias {BookEKM}R Documentation

Relationships with mixtures

Description

The likelihood for relationships problems with mixture and reference profiles is calculated

Usage

mix3Familias(pedigrees, locus, datamatrix, kinship = 0)

Arguments

pedigrees

pedigrees A list of Familias pedigrees

locus

A Familias locus

datamatrix

Each line corresponds to one constellation of geneotypes for the individuals

kinship

Theta parameter

Value

The likelihoods for the pedigrees and detailed output for each term in the sum

Author(s)

Thore Egeland <Thore.Egeland@nmbu.no>

References

Egeland, Kling, Mostad (2015)

Examples

require(Familias)
persons <- c( "CH", "MO", "AF")
ped1 <- pedigree( id = persons, dadid = c( "AF", NA, NA), 
                  momid = c( "MO", NA, NA), 
sex <- c( "male", "female", "male"))
ped2 <- pedigree( id = c( persons, "TF"), 
                  dadid = c( "TF", NA, NA, NA), 
                  momid =c ( "MO", NA, NA, NA), 
                  sex =c ( "male", "female", "male", "male"))
pedigrees <- list( isFather = ped1, unrelated = ped2)
E <- 1:3 ; gAF <- c( 3,4)
datamatrix <- generate( E, K = NULL, 2)
AF <- rep( gAF, dim(datamatrix)[2]/2)
datamatrix <- rbind(datamatrix,AF)
datamatrix <- as.data.frame(datamatrix)
rownames(datamatrix)[c(1,2)] = c( "CH", "MO")
R <- 0.01
theta <- 0.01
locus <- FamiliasLocus( frequencies = rep( 0.2, 5), name = "V1",  
                        allelenames = c( 1:5),
                        femaleMutationRate = R, maleMutationRate = R)
mix3Familias( pedigrees, locus, datamatrix)

[Package BookEKM version 1.0 Index]