Likelihoods for DNA mixtures with dropout and dropin

Computes the likelihood of a mixture conditioned on a given number of known and unknown contributors, and drop-in and dropout probabilities.

Usage

mixLikDrop(R, G, D, di = 0, alleleNames, afreq)

Arguments

R

Vector of mixture alleles

G

List of genotypes. Each element is a vector with genotype for one individual

D

List of dropout values (between 0 and 1) per contributor. Each element is a vector containing heterozygous and homozygous dropout probability for the given contributor

di

Drop-in value (between 0 and 1)

alleleNames

Vector of allele names for the marker

afreq

Vector of allele frequencies for the marker

Value

The likelihood (a numeric)

References

The model is specified in the appendix of Haned et al. (2012) <doi:10.1016/j.fsigen.2012.08.008>.

See also

relMix

Author

Guro Dorum

Examples

#Define alleles and frequencies
alleles <- 1:2
afreq <- c(0.5,0.5)
#Genotypes
gM <- c(1,1)
gC <- c(1,2)
#Mixture alleles
R <- c(1,2)
#Dropout and drop-in values
d <- 0.1
di <- 0.05
#No drop-in for first contributor
D <- list(c(0,0),c(d,d^2))
mixLikDrop(R=R,G=list(gM,gC),D=D,di=di,alleleNames=alleles,afreq=afreq)
#> [1] 0.9025