loop.rpt.IBD: Analysis of DNA mixtures with familial relationships by...

In KinMixLite: Inference About Relationships from DNA Mixtures

Analysis of DNA mixtures with familial relationships by looping

Description

Analysis of DNA mixtures with familial relationships, by looping over traces, markers, and IBD patterns, to reduce total BN table size, at some price in execution time

Usage

loop.rpt.IBD(listdata, pars, IBD, typed.gts = NULL, inds = 1, 
    jtyped = ncol(IBD$patt)/2 - length(typed.gts) + seq_along(typed.gts), 
    jcontr = seq_along(inds), targets = NULL, contribs, 
    quiet=FALSE, verbose=FALSE, presence.only=FALSE, ...) 

Arguments

listdata	as in call to DNAmixture
pars	parameter structure, in mixpar format
IBD	multi-person coefficients of identity, in any of the formats accepted by convertIBD
typed.gts, inds, jtyped, jcontr, targets, contribs, quiet	as in call to rpt.IBD
verbose	should per-marker and overall log10LR's be reported?
presence.only	Set to TRUE to ignore peak heights and evaluate the likelihood function considering peak presence and absence (heights above and below threshold) only. Defaults to FALSE.
...	other arguments to DNAmixture, particularly including k, C, database

Value

The value of the overall log10 LR, and the contributions of individual markers in the form of a vector-valued attribute 'log10LR', are returned invisibly; individual marker/pattern values are also printed out.

Author(s)

Peter Green ([e-mail])

Examples

data(test2data)
data(NGMDyes)

C<-0.001

## Fit 3-person mixture - baseline model

mixD<-DNAmixture(list(epg),k=3,C=rep(list(C),length(list(epg))),database=db)
pars3<-mixpar(rho=list(2),eta=list(100),xi=list(0.1),phi=list(c(U1=0.6,U2=0.3,U3=0.1)))
baseline3<-logL(mixD)(pars3)
size(mixD)

## Fit 3-person mixture - in which U1 and U2 have a parent-child relationship

mixD<-DNAmixture(list(epg),k=3,C=rep(list(C),length(list(epg))),database=db,
	triangulate=FALSE,compile=FALSE)
delete.DQnodes(mixD)
rpt.IBD(mixD,IBD=c(0,1,0),typed.gts=list(),inds=1:2,jtyped=NULL)
size(mixD)
log10LR<-(logL(mixD)(pars3)-baseline3)/log(10)
cat('log10 LR',log10LR,'\n')

## the same analysis by loop.rpt.IBD

listdata<-list(epg)
print(loop.rpt.IBD(listdata,pars3,IBD=c(0,1,0),
	k=3,C=rep(list(C),length(listdata)),database=db,
	typed.gts=list(),inds=1:2,jtyped=NULL))

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