mix3Familias {BookEKM} | R Documentation |
The likelihood for relationships problems with mixture and reference profiles is calculated
mix3Familias(pedigrees, locus, datamatrix, kinship = 0)
pedigrees |
|
locus |
A Familias locus |
datamatrix |
Each line corresponds to one constellation of geneotypes for the individuals |
kinship |
Theta parameter |
The likelihoods for the pedigrees and detailed output for each term in the sum
Thore Egeland <Thore.Egeland@nmbu.no>
Egeland, Kling, Mostad (2015)
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)