R: Likelihood per locus of the observed alleles in a DNA mixture...
lik.loc
R Documentation
Likelihood per locus of the observed alleles in a DNA mixture conditional on the number of contributors
to the mixture
Description
The lik.loc function computes the likelihood of the observed data in a forensic DNA mixture, for each of the loci involved, conditional on the number of contributors to
the mixture.
a simumix object which contains the mixture to be analyzed
freq
a tabfreq object from which to extract the allele frequencies
refpop
a factor giving the reference population in tabfreq from which to
extract the allele frequencies
theta
a float from [0,1[ giving Wright's Fst coefficien. theta
acounts for population subdivision while computing the likelihood of the data.
loc
the loci for which the likelihood shall be computed. Default (set to NULL) corresponds to all loci.
Details
lik.loc computes the likelihood per locus of the observed alleles.
This function implements the general formula for the interpretation
of DNA mixtures in case of subdivided populations (Curran et al, 1999), in the particular case where all contributors
are unknown and belong to the same subpopulation.
The Fst coefficient given in the theta argument allows accounting for population subdivision when all
contributors belong to the same subpopulation.
Value
The function lik.loc returns a vector, of length the number of loci in loc,
giving the likelihood of the data for each locus.
Author(s)
Hinda Haned <h.haned@nfi.minvenj.nl>
References
Haned H, Pene L, Lobry JR, Dufour AB, Pontier D.
Estimating the number of contributors to forensic DNA mixtures: Does maximum likelihood
perform better than maximum allele count? J Forensic Sci, accepted 2010.
Curran JM, Triggs CM, Buckleton J, Weir BS.
Interpreting DNA Mixtures in Structured Populations. J Forensic Sci 1999;44(5): 987-995
See Also
lik for the overall loci likelihood, likestim and
likestim.loc for the estimation of the number of contributors to a DNA mixture through
likelihood maximization
Examples
data(strusa)
#simulation of 1000 genotypes from the Caucasian allele frequencies
gen<-simugeno(strusa,n=c(0,100,0))
#4-person mixture
mix4 <- simumix(gen,ncontri=c(0,4,0))
lik.loc(x=2,mix4, strusa, refpop="Cauc")
lik.loc(x=2,mix4, strusa, refpop="Afri")
#You may also want to try:
#likestim(mix4,strusa,refpop="Cauc")