Likelihood for mixtures that may have related contributors and dropin and dropout of alleles
Description
Likelihood for mixtures that may have related contributors and dropin and dropout of alleles. For a general description of the problem, see see paraMix
. As opposed to paraMix
, dropin and dropout of alleles are allowed. The likelihood is based on simulations from an urn model. Possible mixtures are simulated by applying dropin and dropout to genotypes for the assumed contributors. Genotypes for unknown contributors are simulated conditioned on the pedigree.
Usage
1 2 
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 dropout applied per allele 
pDI 
Probability of dropin 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 

id.U 
Integers indicating untyped contributors (e.g.,suspect(s)). Only relevant if a pedigree is specified. 
id.V 
Integers indicating typed noncontributors. 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  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

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