Package: KinMixLite 2.1.1

KinMixLite: Inference About Relationships from DNA Mixtures

Methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a 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) <doi:10.1016/j.fsigen.2017.02.001> and Green, P. J. and Mortera, J. (2021) <doi:10.1111/rssc.12498>.

Authors:Peter Green [aut, cre]

KinMixLite_2.1.1.tar.gz
KinMixLite_2.1.1.zip(r-4.5)KinMixLite_2.1.1.zip(r-4.4)KinMixLite_2.1.1.zip(r-4.3)
KinMixLite_2.1.1.tgz(r-4.4-any)KinMixLite_2.1.1.tgz(r-4.3-any)
KinMixLite_2.1.1.tar.gz(r-4.5-noble)KinMixLite_2.1.1.tar.gz(r-4.4-noble)
KinMixLite_2.1.1.tgz(r-4.4-emscripten)KinMixLite_2.1.1.tgz(r-4.3-emscripten)
KinMixLite.pdf |KinMixLite.html
KinMixLite/json (API)

# Install 'KinMixLite' in R:
install.packages('KinMixLite', repos = c('https://petergreen5678.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Cgt - Small data set for demonstrating some capabilities of KinMix and KinMixLite
  • Fgt - Small data set for demonstrating some capabilities of KinMix and KinMixLite
  • Mgt - Small data set for demonstrating some capabilities of KinMix and KinMixLite
  • Rgt - Small data set for demonstrating some capabilities of KinMix and KinMixLite
  • S1gt - Small data set for demonstrating some capabilities of KinMix and KinMixLite
  • S2gt - Small data set for demonstrating some capabilities of KinMix and KinMixLite
  • db - Small data set for demonstrating some capabilities of KinMix and KinMixLite
  • emperors - IBD pattern distribution in the Iulius-Claudius pedigree
  • epg - Small data set for demonstrating some capabilities of KinMix and KinMixLite

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 338 downloads 34 exports 49 dependencies

Last updated 1 months agofrom:a05e07e1dc. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winOKNov 09 2024
R-4.5-linuxOKNov 09 2024
R-4.4-winOKNov 09 2024
R-4.4-macOKNov 09 2024
R-4.3-winOKNov 09 2024
R-4.3-macOKNov 09 2024

Exports:add.child.meiosis.nodesadd.motherchild.likd.nodeadd.relative.likd.nodeas.gtas.IBDcheckpeaksconvertIBDdelete.DQnodesexpr.make.findingsgt2acaintoMixlogL.UKXlogLXloop.rpt.IBDmake.profilemixMLXpedigreeIBDplot.IBDprotectedprotected.mixMLreplace.tables.for.UAFreplace.Ui.tablesrequire.compiledrGTsrnirpt.AMELrpt.IBDrpt.typed.childrpt.typed.parentsrpt.typed.relativerpt.typed.relativesrpt.UAFsizewlr

Dependencies:backportsbroomclicodacpp11DNAmixturesLitedplyrevaluatefansigenericsgluegRaingRavengRbasehighrigraphkinship2knitrlatticelifecyclemagrittrMatrixnumDerivpedmutpedtoolspillarpkgconfigpurrrquadprogR6RcppRcppArmadilloRcppEigenribdrlangRsolnpslamstatnet.commonstringistringrtibbletidyrtidyselecttruncnormutf8vctrswithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Inference About Relationships from DNA MixturesKinMixLite-package KinMixLite
Replace CPTs for mixture contributor a Father, given Child genotype, by MBN methodadd.child.meiosis.nodes
Replace CPTs for mixture contributor a Father, given Child and Mother genotypes, by ALN methodadd.motherchild.likd.node
Replace CPTs for mixture contributor a Father, given Child genotype, by ALN methodadd.relative.likd.node
Extract genotype profile for a single contributor from rGTs outputas.gt
Check and modify database to have positive frequencies for all observed peaks/allelescheckpeaks
Convert relationship information to IBD pattern distributionas.IBD convertIBD
Delete D and Q dummy nodes from all Bayes nets in mixturedelete.DQnodes
IBD pattern distribution in the Iulius-Claudius pedigreeemperors
Coding additional findings as expressionexpr.make.findings
Formatsformats
Converts genotype profiles to allele count arraysgt2aca
Edit output from rGTs to omit individuals with NA amounts of DNAintoMix
Evaluates mixture log likelihood for unknown contributors with extra findingslogL.UKX
Evaluates mixture log likelihood when extra findings presentlogLX
Analysis of DNA mixtures with familial relationships by loopingloop.rpt.IBD
Convert genotype profile to reference profile formatmake.profile
Maximises mixture likelihood when extra findings presentmixMLX
Construct IBD pattern distribution from pedigreepedigreeIBD
Plot IBD patterns and pattern distributionsplot.IBD
Catch numerical errors, and return -Infprotected
Protect against numerical errors in maximum likelihood computationprotected.mixML
Force compilation of all BNs in a DNA mixture modelrequire.compiled
Simulate random genotype profiles and DNA samples for related individualsrGTs
Random number initialiser supporting spontaneous replicationrni
Replace CPTs for AMEL marker in a DNA mixturerpt.AMEL
Replacing CPTs for selected mixture contributors with familial relationshipsreplace.Ui.tables rpt.IBD rpt.typed.child rpt.typed.parents rpt.typed.relative rpt.typed.relatives
Replace CPTs in a DNA mixture to model uncertain allele frequenciesreplace.tables.for.UAF rpt.UAF
Calculate and display total size of BN tables for a DNA mixturesize
Small data set for demonstrating some capabilities of KinMix and KinMixLiteCgt db epg Fgt Mgt Rgt S1gt S2gt test2data
Computes paternity LR using WLR methodwlr