Package: GeneticsPed 1.69.0

David Henderson

GeneticsPed: Pedigree and genetic relationship functions

Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care!

Authors:Gregor Gorjanc and David A. Henderson <[email protected]>, with code contributions by Brian Kinghorn and Andrew Percy

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NEWS

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:GeneticsPed-1.67.0(bioc 3.20)GeneticsPed-1.66.0(bioc 3.19)

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

genetics

3.82 score 11 scripts 248 downloads 28 exports 6 dependencies

Last updated 23 days agofrom:48e7cabac9. Checks:OK: 1 WARNING: 5 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64WARNINGOct 30 2024
R-4.5-linux-x86_64WARNINGOct 30 2024
R-4.4-win-x86_64WARNINGOct 30 2024
R-4.4-mac-x86_64WARNINGOct 30 2024
R-4.4-mac-aarch64WARNINGSep 01 2024
R-4.3-win-x86_64NOTEOct 30 2024
R-4.3-mac-x86_64NOTEOct 30 2024
R-4.3-mac-aarch64NOTESep 01 2024

Exports:as.PedigreecheckcheckIdextendfamilyfamily<-gameteFlowMgeneContributiongeneFlowTgeneFlowTinvgeneratePedigreegenerationgeneration<-gpigpLong2WidehwpinbreedinginverseAdditiveis.PedigreeisFounderkinshipmendelianSamplingDnIndividualPedigreeprunerelationshipAdditiveremoveIndividualsummary.Pedigree

Dependencies:combinatgdatageneticsgtoolsMASSmvtnorm

Calculation of genetic relatedness/relationship between individuals in the pedigree

Rendered fromgeneticRelatedness.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2013-11-01
Started: 2013-11-01

Pedigree handling

Rendered frompedigreeHandling.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2013-11-01
Started: 2013-11-01

Quantitative genetic (animal) model example in R

Rendered fromquanGenAnimalModel.Rnwusingutils::Sweaveon Oct 30 2024.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Check consistency of data in pedigreecheck check.Pedigree checkId
Extend pedigreeextend
Find families (lines) in the pedigreefamily family<-
Gene contribution or proportion of genes in pedigree by individualgeneContribution
Gene and gamete flow matricesgameteFlowM geneFlowT geneFlowTinv mendelianSamplingD
Generate Pedigree examplegeneratePedigree
Calculate generation valuegeneration generation<-
Genotype probability indexgpi
Utility functions for gpi()gpLong2Wide hwp
Inbreeding coefficientinbreeding
Founder and non-founder individuals in the pedigreeisFounder
Model matrix for individuals with and without recordsmodel.matrix.Pedigree
Pedigree and data examplesFalconer Falconer5.1 Mrode Mrode2.1 Mrode3.1
Number of individuals in a pedigreenIndividual
Pedigreeas.character.Pedigree as.factor.Pedigree as.integer.Pedigree as.Pedigree as.Pedigree.data.frame as.Pedigree.matrix as.Pedigree.Pedigree is.Pedigree Pedigree
Prune pedigreeprune
Additive relationship matrix and its inverseinverseAdditive kinship relationshipAdditive
Remove individual from pedigreeremoveIndividual
Sort pedigreesort.Pedigree
Pedigree summarysummary.Pedigree
Undocumented functionsundocumented