Package: GeneticsPed 1.74.0

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

GeneticsPed_1.74.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeneticsPed/json (API)

# Install 'GeneticsPed' in R:
install.packages('GeneticsPed', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:GeneticsPed-1.75.0(bioc 3.24)GeneticsPed-1.74.0(bioc 3.23)

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

geneticscpp

4.01 score 17 scripts 450 downloads 1 mentions 28 exports 6 dependencies

Last updated from:340b6a27f6 (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 1 OK, 7 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR156
linux-devel-arm64WARNING145
linux-devel-x86_64WARNING207
source / vignettesOK184
linux-release-arm64WARNING124
linux-release-x86_64WARNING221
macos-release-arm64FAIL77
macos-release-x86_64FAIL139
macos-oldrel-arm64FAIL75
macos-oldrel-x86_64FAIL148
windows-devel-arm64FAIL145
windows-devel-x86_64WARNING144
windows-release-arm64FAIL156
windows-release-x86_64WARNING167
windows-oldrel-x86_64WARNING98
wasm-releaseFAIL102

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

Dependencies:combinatgdatageneticsgtoolsMASSmvtnorm

Calculation of genetic relatedness/relationship between individuals in the pedigree
Rendered fromgeneticRelatedness.Rnwusingutils::Sweave

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

Pedigree handling
Check consistency of data in pedigree
Rendered frompedigreeHandling.Rnwusingutils::Sweave

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

Quantitative genetic (animal) model example in R
Rendered fromquanGenAnimalModel.Rnwusingutils::Sweave

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