Likelihood for mixtures that may have related contributors and drop-in and drop-out of alleles

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Description

Likelihood for mixtures that may have related contributors and drop-in and drop-out of alleles. For a general description of the problem, see see paraMix. As opposed to paraMix, drop-in and drop-out of alleles are allowed. The likelihood is based on simulations from an urn model. Possible mixtures are simulated by applying drop-in and drop-out to genotypes for the assumed contributors. Genotypes for unknown contributors are simulated conditioned on the pedigree.

Usage

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simLR(R, x, alleles, afreq, pDO, pDI, N, known_genotypes = NULL, 
ped = NULL, id.U = NULL, id.V = NULL)

Arguments

R

Integers, mixture

x

Number of unknown contributors

alleles

Integers indicating alleles for marker

afreq

A numerical vector with allele frequencies

pDO

Probability of drop-out applied per allele

pDI

Probability of drop-in per locus

N

Number of simulations

known_genotypes

List of known genotypes. If a pedigree is specified, each element must a triplet of integers corresponding to (id,allele1,allele2). If no pedigree is specified, the id can be omitted.

ped

linkdat object, or a list of such (if disconnected), describing the claimed relationship.

id.U

Integers indicating untyped contributors (e.g.,suspect(s)). Only relevant if a pedigree is specified.

id.V

Integers indicating typed non-contributors. Only relevant if a pedigree is specified.

Value

p.R: the likelihood of the mixture R

Author(s)

Guro Dorum and Thore Egeland <guro.dorum@nmbu.no>

See Also

See paraMix.

Examples

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require(paramlink)
alleles <-1:4
p <- c(0.044, 0.166, 0.11, 0.68)
names(p) <- alleles
R <- 1:3
known <- list(c(6,1,2),c(4,3,3))
x <- halfCousinPed(0)
y <- singleton(6,sex=2)
pDO <- 0.1
pDI <- 0.05
N <- 20000
lp <- simLR(R=R, x=0, alleles=alleles, afreq=p, 
pDO, pDI, N, known_genotypes=known, ped=list(x,y))
ld <- simLR(R=R, x=1, alleles=alleles, afreq=p, pDO, pDI, 
N, known_genotypes=known, ped=list(x,y), id.U=5,id.V=4)
lp/ld