GeneticsPed: Pedigree and genetic relationship functions
Version 1.38.1

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!

Browse man pages Browse package API and functions Browse package files

AuthorGregor Gorjanc and David A. Henderson <DNADavenator@GMail.Com>, with code contributions by Brian Kinghorn and Andrew Percy (see file COPYING)
Bioconductor views Genetics
Date of publicationNone
MaintainerDavid Henderson <DNADavenator@GMail.Com>
LicenseLGPL (>= 2.1) | file LICENSE
Version1.38.1
URL http://rgenetics.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneticsPed")

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

Functions

"[.Pedigree" Man page
Falconer Man page
Falconer5.1 Man page
Mrode Man page
Mrode2.1 Man page
Mrode3.1 Man page
Pedigree Man page Source code
as.Pedigree Man page Source code
as.Pedigree.Pedigree Man page Source code
as.Pedigree.data.frame Man page Source code
as.Pedigree.matrix Man page Source code
as.character.Pedigree Man page
as.factor.Pedigree Man page
as.integer.Pedigree Man page
ascendantEqualAscendant Source code
ascendantInAscendant Source code
check Man page Source code
check.Pedigree Man page Source code
checkAttributes Source code
checkId Man page Source code
checkSex Source code
dropLevels Source code
extend Man page Source code
family Man page Source code
family<- Man page
gameteFlowM Man page Source code
geneContribution Man page Source code
geneFlowT Man page Source code
geneFlowTinv Man page Source code
generatePedigree Man page Source code
generation Man page Source code
generation<- Man page
getAscendant Source code
getAscendantLevel Source code
getAscendantName Source code
getAscendantSex Source code
getChecked Source code
getCoded Source code
getColClass Source code
getDtBirth Source code
getDtBirthName Source code
getExtended Source code
getFamily Source code
getFamilyName Source code
getFather Source code
getFatherName Source code
getGeneration Source code
getGenerationName Source code
getGenerationOrder Source code
getId Source code
getIdName Source code
getMother Source code
getMotherName Source code
getSex Source code
getSexName Source code
getSorted Source code
getUnknown Source code
gpLong2Wide Man page Source code
gpi Man page Source code
hwp Man page Source code
idClass Source code
idEqualAscendant Source code
idIsNA Source code
idNotUnique Source code
inbreeding Man page Source code
inverseAdditive Man page Source code
is.Pedigree Man page Source code
isFounder Man page Source code
kinship Man page Source code
mendelianSamplingD Man page Source code
model.matrix.Pedigree Man page Source code
nIndividual Man page Source code
prune Man page Source code
relationshipAdditive Man page Source code
removeIndividual Man page Source code
sort.Pedigree Man page Source code
summary.Pedigree Man page Source code
undocumented Man page
unusedLevels Source code
writeMendel Source code
writePreMakeped Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/TDT.R
R/buildPedigree.R
R/check.pedigree.R
R/extend.R
R/family.R
R/founder.R
R/geneContribution.R
R/generateData.R
R/generatePedigree.R
R/generation.R
R/getSlot.R
R/gpi.R
R/inbreeding.R
R/inverseAdditive.R
R/model.matrix.R
R/nIndividual.R
R/pedigree.R
R/prune.R
R/relationshipAdditive.R
R/removeIndividual.R
R/sort.pedigree.R
R/summary.pedigree.R
R/writePedigree.R
build
build/vignette.rds
data
data/Falconer5.1.csv
data/Mrode2.1.csv
data/Mrode3.1.csv
include
include/ainverse.h
include/eibd.h
include/inbreed.h
include/math_utilities.h
include/meuwissen.h
include/pedSort.h
include/pedtemplate.h
include/sortped.h
inst
inst/NEWS
inst/TODO
inst/doc
inst/doc/geneticRelatedness.R
inst/doc/geneticRelatedness.Rnw
inst/doc/geneticRelatedness.pdf
inst/doc/pedigreeHandling.R
inst/doc/pedigreeHandling.Rnw
inst/doc/pedigreeHandling.pdf
inst/doc/quanGenAnimalModel.R
inst/doc/quanGenAnimalModel.Rnw
inst/doc/quanGenAnimalModel.pdf
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/runit.extend.R
inst/unitTests/runit.genRelMatrix.R
inst/unitTests/runit.gpi.R
inst/unitTests/runit.pedigree.R
inst/unitTests/runit.prune.R
inst/unitTests/runit.unknown.R
man
man/TDT.Rd
man/check.Rd
man/datasets.Rd
man/extend.Rd
man/family.Rd
man/founder.Rd
man/geneContribution.Rd
man/generatePedigree.Rd
man/generation.Rd
man/gpi.Rd
man/gpiUtil.Rd
man/inbreeding.Rd
man/model.matrix.Rd
man/nIndividual.Rd
man/pedigree.Rd
man/prune.Rd
man/relationshipAdditive.Rd
man/removeIndividual.Rd
man/sort.pedigree.Rd
man/summary.pedigree.Rd
man/undocumented.Rd
src
src/ainverse.cc
src/eibd.cc
src/ggmatmult.f
src/gpi.f
src/inbreed.cc
src/inverseAdditive.cc
src/meuwissen.cc
src/pedSort.cc
src/pedtemplate.cc
src/register.cc
src/sargolzaei.c
src/sortped.cc
tests
tests/doRUnit.R
vignettes
vignettes/geneticRelatedness.Rnw
vignettes/library.bib
vignettes/pedigreeHandling.Rnw
vignettes/quanGenAnimalModel.Rnw
GeneticsPed documentation built on May 20, 2017, 9:20 p.m.