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!

AuthorGregor Gorjanc and David A. Henderson <DNADavenator@GMail.Com>, with code contributions by Brian Kinghorn and Andrew Percy (see file COPYING)
Date of publicationNone
MaintainerDavid Henderson <DNADavenator@GMail.Com>
LicenseLGPL (>= 2.1) | file LICENSE
Version1.36.0
http://rgenetics.org

View on Bioconductor

Functions

as.character.Pedigree Man page
as.factor.Pedigree Man page
as.integer.Pedigree Man page
as.Pedigree Man page
as.Pedigree.data.frame Man page
as.Pedigree.matrix Man page
as.Pedigree.Pedigree Man page
check Man page
checkId Man page
check.Pedigree Man page
extend Man page
Falconer Man page
Falconer5.1 Man page
family Man page
family<- Man page
gameteFlowM Man page
geneContribution Man page
geneFlowT Man page
geneFlowTinv Man page
generatePedigree Man page
generation Man page
generation<- Man page
gpi Man page
gpLong2Wide Man page
hwp Man page
inbreeding Man page
inverseAdditive Man page
isFounder Man page
is.Pedigree Man page
kinship Man page
mendelianSamplingD Man page
model.matrix.Pedigree Man page
Mrode Man page
Mrode2.1 Man page
Mrode3.1 Man page
nIndividual Man page
Pedigree Man page
"[.Pedigree" Man page
prune Man page
relationshipAdditive Man page
removeIndividual Man page
sort.Pedigree Man page
summary.Pedigree Man page
undocumented Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.