add.motherchild.likd.node: Replace CPTs for mixture contributor a Father, given Child...

In KinMixLite: Inference About Relationships from DNA Mixtures

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)

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?

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(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') 

KinMixLite documentation built on Oct. 9, 2024, 9:07 a.m.