add.relative.likd.node {KinMixLite}

Replace CPTs for mixture contributor a Father, given Child genotype, 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 only Child genotyped then compile all domains. Implements method ALN.

Usage

add.relative.likd.node(mixture,aca,ind=1)

Arguments

mixture

A compiled DNAmixture object

aca

Child's genotype profile as an allele count array

ind

Index of contributor regarded as Parent (or Child): which ‘unknown’ contributor are we modelling by amending his/her CPTs?

Value

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

Author(s)

Peter Green ([e-mail])

Examples

data(test2data)

# set threshold C
C<-0.001

mixD<-DNAmixture(list(epg),k=2,C=list(C),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)

mixALN<-DNAmixture(list(epg),k=2,C=list(C),database=db,triangulate=FALSE,compile=FALSE)
cgtcaca<-gt2aca(mixALN,Cgt) 
add.relative.likd.node(mixALN,cgtcaca,1)
log10LR<-(logLX(mixALN,
	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')