KinMixLite (version 2.2.1)

add.motherchild.likd.node: Replace CPTs for mixture contributor a Father, given Child and Mother genotypes, by ALN method

Description

loop over markers, and alleles within markers to create node Rlikd for relative likelihood for individual i, for paternity model with Mother and Child genotyped then compile all domains. Implements method ALN.

Usage

add.motherchild.likd.node(mixture,Cgt,Mgt,db,ind=1)

Value

No value is returned, the function is called for its side effect

Arguments

mixture

A DNAmixture object

Cgt

Child's genotype profile as a data frame containing variables marker, allele1 and allele2

Mgt

Mother's genotype profile as a data frame containing variables marker, allele1 and allele2

db

Allele frequency database

ind

Index of contributor regarded as Father: which `unknown' contributor are we modelling by amending his CPTs?

Author

Peter Green ([e-mail])

Examples

data(test2data)

# set threshold C
C<-0.001

mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db)
pars<-mixpar(rho=list(2),eta=list(100),xi=list(0.1),phi=list(c(U1=0.7,U2=0.3)))
baseline<-logL(mixD)(pars)

mixD3<-DNAmixture(list(epg),k=2,C=list(0.001),database=db,triangulate=FALSE,compile=FALSE)
cgtcaca<-gt2aca(mixD3,Cgt) 
add.motherchild.likd.node(mixD3,Cgt,Mgt,db,1)
log10LR<-(logLX(mixD3,
	expr.make.findings(list(
	list('Male',ind=1),
	list('Rlikd',aca='cgtcaca',cgt='Cgt',evid='Revid')
	))
	)(pars)-baseline)/log(10)
cat('log10 LR',log10LR,'\n')