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!

Author
Gregor Gorjanc and David A. Henderson <DNADavenator@GMail.Com>, with code contributions by Brian Kinghorn and Andrew Percy (see file COPYING)
Date of publication
None
Maintainer
David Henderson <DNADavenator@GMail.Com>
License
LGPL (>= 2.1) | file LICENSE
Version
1.36.0
URLs

View on Bioconductor

Man pages

check
Check consistency of data in pedigree
datasets
Pedigree and data examples
extend
Extend pedigree
family
Find families (lines) in the pedigree
founder
Founder and non-founder individuals in the pedigree
geneContribution
Gene contribution or proportion of genes in pedigree by...
generatePedigree
Generate Pedigree example
generation
Calculate generation value
gpi
Genotype probability index
gpiUtil
Utility functions for gpi()
inbreeding
Inbreeding coefficient
model.matrix
Model matrix for individuals with and without records
nIndividual
Number of individuals in a pedigree
pedigree
Pedigree
prune
Prune pedigree
relationshipAdditive
Additive relationship matrix and its inverse
removeIndividual
Remove individual from pedigree
sort.pedigree
Sort pedigree
summary.pedigree
Pedigree summary
TDT
Gene and gamete flow matrices
undocumented
Undocumented functions

Files in this package

GeneticsPed/DESCRIPTION
GeneticsPed/LICENSE
GeneticsPed/NAMESPACE
GeneticsPed/R
GeneticsPed/R/TDT.R
GeneticsPed/R/buildPedigree.R
GeneticsPed/R/check.pedigree.R
GeneticsPed/R/extend.R
GeneticsPed/R/family.R
GeneticsPed/R/founder.R
GeneticsPed/R/geneContribution.R
GeneticsPed/R/generateData.R
GeneticsPed/R/generatePedigree.R
GeneticsPed/R/generation.R
GeneticsPed/R/getSlot.R
GeneticsPed/R/gpi.R
GeneticsPed/R/inbreeding.R
GeneticsPed/R/inverseAdditive.R
GeneticsPed/R/model.matrix.R
GeneticsPed/R/nIndividual.R
GeneticsPed/R/pedigree.R
GeneticsPed/R/prune.R
GeneticsPed/R/relationshipAdditive.R
GeneticsPed/R/removeIndividual.R
GeneticsPed/R/sort.pedigree.R
GeneticsPed/R/summary.pedigree.R
GeneticsPed/R/writePedigree.R
GeneticsPed/build
GeneticsPed/build/vignette.rds
GeneticsPed/data
GeneticsPed/data/Falconer5.1.csv
GeneticsPed/data/Mrode2.1.csv
GeneticsPed/data/Mrode3.1.csv
GeneticsPed/include
GeneticsPed/include/ainverse.h
GeneticsPed/include/eibd.h
GeneticsPed/include/inbreed.h
GeneticsPed/include/math_utilities.h
GeneticsPed/include/meuwissen.h
GeneticsPed/include/pedSort.h
GeneticsPed/include/pedtemplate.h
GeneticsPed/include/sortped.h
GeneticsPed/inst
GeneticsPed/inst/NEWS
GeneticsPed/inst/TODO
GeneticsPed/inst/doc
GeneticsPed/inst/doc/geneticRelatedness.R
GeneticsPed/inst/doc/geneticRelatedness.Rnw
GeneticsPed/inst/doc/geneticRelatedness.pdf
GeneticsPed/inst/doc/pedigreeHandling.R
GeneticsPed/inst/doc/pedigreeHandling.Rnw
GeneticsPed/inst/doc/pedigreeHandling.pdf
GeneticsPed/inst/doc/quanGenAnimalModel.R
GeneticsPed/inst/doc/quanGenAnimalModel.Rnw
GeneticsPed/inst/doc/quanGenAnimalModel.pdf
GeneticsPed/inst/unitTests
GeneticsPed/inst/unitTests/Makefile
GeneticsPed/inst/unitTests/runit.extend.R
GeneticsPed/inst/unitTests/runit.genRelMatrix.R
GeneticsPed/inst/unitTests/runit.gpi.R
GeneticsPed/inst/unitTests/runit.pedigree.R
GeneticsPed/inst/unitTests/runit.prune.R
GeneticsPed/inst/unitTests/runit.unknown.R
GeneticsPed/man
GeneticsPed/man/TDT.Rd
GeneticsPed/man/check.Rd
GeneticsPed/man/datasets.Rd
GeneticsPed/man/extend.Rd
GeneticsPed/man/family.Rd
GeneticsPed/man/founder.Rd
GeneticsPed/man/geneContribution.Rd
GeneticsPed/man/generatePedigree.Rd
GeneticsPed/man/generation.Rd
GeneticsPed/man/gpi.Rd
GeneticsPed/man/gpiUtil.Rd
GeneticsPed/man/inbreeding.Rd
GeneticsPed/man/model.matrix.Rd
GeneticsPed/man/nIndividual.Rd
GeneticsPed/man/pedigree.Rd
GeneticsPed/man/prune.Rd
GeneticsPed/man/relationshipAdditive.Rd
GeneticsPed/man/removeIndividual.Rd
GeneticsPed/man/sort.pedigree.Rd
GeneticsPed/man/summary.pedigree.Rd
GeneticsPed/man/undocumented.Rd
GeneticsPed/src
GeneticsPed/src/ainverse.cc
GeneticsPed/src/eibd.cc
GeneticsPed/src/ggmatmult.f
GeneticsPed/src/gpi.f
GeneticsPed/src/inbreed.cc
GeneticsPed/src/inverseAdditive.cc
GeneticsPed/src/meuwissen.cc
GeneticsPed/src/pedSort.cc
GeneticsPed/src/pedtemplate.cc
GeneticsPed/src/register.cc
GeneticsPed/src/sargolzaei.c
GeneticsPed/src/sortped.cc
GeneticsPed/tests
GeneticsPed/tests/doRUnit.R
GeneticsPed/vignettes
GeneticsPed/vignettes/geneticRelatedness.Rnw
GeneticsPed/vignettes/library.bib
GeneticsPed/vignettes/pedigreeHandling.Rnw
GeneticsPed/vignettes/quanGenAnimalModel.Rnw