mixLikDrop: Likelihoods for DNA mixtures with dropout and dropin

In gdorum/relMix: Relationship Inference for DNA Mixtures

Likelihoods for DNA mixtures with dropout and dropin

Description

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

Author(s)

Guro Dorum

References

The model is specified in the appendix of Haned et al. (2012) Exploratory data analysis for the interpretation of low template DNA mixtures, FSI Genetics Dec;6(6):762-74

See Also

relMix

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)

gdorum/relMix documentation built on April 17, 2024, 8:49 p.m.