add.child.meiosis.nodes: 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 genotype, by MBN method

Description

loop over markers, and alleles within markers to create nodes for child allele count nodes, for paternity model with only Child genotyped then compile all domains. Implements method MBN.

Usage

add.child.meiosis.nodes(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?

Details

To calculate the likelihood of this model, conditional on the child's genotype, a call to this function should be followed by (a) setting the finding of the child's genotype by defining extra.findings, (b) evaluating the loglikelihood using logLX, and (c) correcting the result by subtracting the log probability of the child's genotype, all as in the example below. Without (c), the value returned is the likelihood for the peak heights and the child's genotype.

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)

mixMBN<-DNAmixture(list(epg),k=2,C=list(C),database=db,triangulate=FALSE,compile=FALSE)
cgtcaca<-gt2aca(mixMBN,Cgt)
add.child.meiosis.nodes(mixMBN,cgtcaca,1)
log10LR<-(logLX(mixMBN,
	expr.make.findings(list(
	list('Male',ind=1),
	list('Caca',aca='cgtcaca')
	))
	)(pars)-attr(cgtcaca,'logGt')-baseline)/log(10)
cat('log10 LR',log10LR,'\n')  

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