R: Inference About Relationships from DNA Mixtures

# Inference About Relationships from DNA Mixtures

## Documentation for package ‘KinMixLite’ version 2.2.1

- DESCRIPTION file
- Code demos. Use demo() to run them.

## Help Pages

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
checkdata | Check data for absences of markers or allele values
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
KinMix | Create a DNA mixture model, with possibly related contributors
KinMixLite | Inference About Relationships from DNA Mixtures
logL.UKX | Evaluates mixture log likelihood for unknown contributors with extra findings
logLm | Log likelihood for mixture model, by marker
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
make.profiles | 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