| add.child.meiosis.nodes {KinMixLite} | R Documentation |
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 (P.J.Green@bristol.ac.uk)
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')