Inference About Relationships from DNA Mixtures

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Documentation for package ‘KinMixLite’ version 2.1.1

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KinMixLite-package Inference About Relationships from DNA Mixtures
add.child.meiosis.nodes Replace CPTs for mixture contributor a Father, given Child genotype, by MBN method
add.motherchild.likd.node Replace CPTs for mixture contributor a Father, given Child and Mother genotypes, by ALN method
add.relative.likd.node Replace CPTs for mixture contributor a Father, given Child genotype, by ALN method
as.gt Extract genotype profile for a single contributor from rGTs output
as.IBD Convert relationship information to IBD pattern distribution
Cgt Small data set for demonstrating some capabilities of KinMix and KinMixLite
checkpeaks Check and modify database to have positive frequencies for all observed peaks/alleles
convertIBD Convert relationship information to IBD pattern distribution
db Small data set for demonstrating some capabilities of KinMix and KinMixLite
delete.DQnodes Delete D and Q dummy nodes from all Bayes nets in mixture
emperors IBD pattern distribution in the Iulius-Claudius pedigree
epg Small data set for demonstrating some capabilities of KinMix and KinMixLite
expr.make.findings Coding additional findings as expression
Fgt Small data set for demonstrating some capabilities of KinMix and KinMixLite
formats Formats
gt2aca Converts genotype profiles to allele count arrays
intoMix Edit output from rGTs to omit individuals with NA amounts of DNA
KinMixLite Inference About Relationships from DNA Mixtures
logL.UKX Evaluates mixture log likelihood for unknown contributors with extra findings
logLX Evaluates mixture log likelihood when extra findings present
loop.rpt.IBD Analysis of DNA mixtures with familial relationships by looping
make.profile Convert genotype profile to reference profile format
Mgt Small data set for demonstrating some capabilities of KinMix and KinMixLite
mixMLX Maximises mixture likelihood when extra findings present
pedigreeIBD Construct IBD pattern distribution from pedigree
plot.IBD Plot IBD patterns and pattern distributions
protected Catch numerical errors, and return -Inf
protected.mixML Protect against numerical errors in maximum likelihood computation
replace.tables.for.UAF Replace CPTs in a DNA mixture to model uncertain allele frequencies
replace.Ui.tables Replacing CPTs for selected mixture contributors with familial relationships
require.compiled Force compilation of all BNs in a DNA mixture model
Rgt Small data set for demonstrating some capabilities of KinMix and KinMixLite
rGTs Simulate random genotype profiles and DNA samples for related individuals
rni Random number initialiser supporting spontaneous replication
rpt.AMEL Replace CPTs for AMEL marker in a DNA mixture
rpt.IBD Replacing CPTs for selected mixture contributors with familial relationships
rpt.typed.child Replacing CPTs for selected mixture contributors with familial relationships
rpt.typed.parents Replacing CPTs for selected mixture contributors with familial relationships
rpt.typed.relative Replacing CPTs for selected mixture contributors with familial relationships
rpt.typed.relatives Replacing CPTs for selected mixture contributors with familial relationships
rpt.UAF Replace CPTs in a DNA mixture to model uncertain allele frequencies
S1gt Small data set for demonstrating some capabilities of KinMix and KinMixLite
S2gt Small data set for demonstrating some capabilities of KinMix and KinMixLite
size Calculate and display total size of BN tables for a DNA mixture
test2data Small data set for demonstrating some capabilities of KinMix and KinMixLite
wlr Computes paternity LR using WLR method