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KinMixLite (version 2.2.0)

Inference About Relationships from DNA Mixtures

Description

Methods for inference about/under complex relationships using peak height data from DNA mixtures: the most basic example would be testing whether a contributor to a mixture is the father of a child of known genotype. This provides most of the functionality of the 'KinMix' package, but with some loss of efficiency and restriction on problem size, as the latter uses 'RHugin' as the Bayes net engine, while this package uses 'gRain'. The package implements the methods introduced in Green, P. J. and Mortera, J. (2017) and Green, P. J. and Mortera, J. (2021) .

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Version

Install

install.packages('KinMixLite')

Monthly Downloads

335

Version

2.2.0

License

GPL (>= 2)

Maintainer

Peter Green

Last Published

July 15th, 2025

Functions in KinMixLite (2.2.0)

logLX

Evaluates mixture log likelihood when extra findings present
loop.rpt.IBD

Analysis of DNA mixtures with familial relationships by looping
rGTs

Simulate random genotype profiles and DNA samples for related individuals
mixMLX

Maximises mixture likelihood when extra findings present
make.profile

Convert genotype profile to reference profile format
rpt.IBD

Replacing CPTs for selected mixture contributors with familial relationships
rni

Random number initialiser supporting spontaneous replication
size

Calculate and display total size of BN tables for a DNA mixture
protected

Catch numerical errors, and return -Inf
logL.UKX

Evaluates mixture log likelihood for unknown contributors with extra findings
protected.mixML

Protect against numerical errors in maximum likelihood computation
intoMix

Edit output from rGTs to omit individuals with NA amounts of DNA
pedigreeIBD

Construct IBD pattern distribution from pedigree
plot.IBD

Plot IBD patterns and pattern distributions
rpt.UAF

Replace CPTs in a DNA mixture to model uncertain allele frequencies
wlr

Computes paternity LR using WLR method
require.compiled

Force compilation of all BNs in a DNA mixture model
rpt.AMEL

Replace CPTs for AMEL marker in a DNA mixture
test2data

Small data set for demonstrating some capabilities of KinMix and KinMixLite
checkdata

Check data for absences of markers or allele values
checkpeaks

Check and modify database to have positive frequencies for all observed peaks/alleles
add.child.meiosis.nodes

Replace CPTs for mixture contributor a Father, given Child genotype, by MBN method
delete.DQnodes

Delete D and Q dummy nodes from all Bayes nets in mixture
convertIBD

Convert relationship information to IBD pattern distribution
add.motherchild.likd.node

Replace CPTs for mixture contributor a Father, given Child and Mother genotypes, by ALN method
emperors

IBD pattern distribution in the Iulius-Claudius pedigree
expr.make.findings

Coding additional findings as expression
as.gt

Extract genotype profile for a single contributor from rGTs output
add.relative.likd.node

Replace CPTs for mixture contributor a Father, given Child genotype, by ALN method
KinMixLite-package

tools:::Rd_package_title("KinMixLite")
formats

Formats
gt2aca

Converts genotype profiles to allele count arrays
KinMix

Create a DNA mixture model, with possibly related contributors