Likelihoods for DNA mixtures with dropout and dropin

Share:

Description

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

Usage

1
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

alleleNames

Vector of allele names for the marker

afreq

Vector of allele frequencies for the marker

Value

Returns a 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
#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)