optiSel: Optimum Contribution Selection and Population Genetics

A framework for the optimization of breeding programs via optimum contribution selection. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.

Install the latest version of this package by entering the following in R:
install.packages("optiSel")
AuthorRobin Wellmann
Date of publication2017-04-15 06:36:35 UTC
MaintainerRobin Wellmann <r.wellmann@uni-hohenheim.de>
LicenseGPL-2
Version0.7.1

View on CRAN

Man pages

Cattle: Phenotypes of Genotyped Cattle

Chr1.phased: Phased Cattle Genotypes from Chromosome 1

Chr2.phased: Phased Cattle Genotypes from Chromosome 2

completeness: Calculates Pedigree Completeness

conttac: Calculates *Cont*ributions *T*o *A*ge *C*ohorts

ExamplePed: Pedigree of Hinterwald Cattle

freqlist: Combines Objects Computed with Function haplofreq() into a...

genecont: Calculates Genetic Contributions using Pedigrees.

haplofreq: Evaluates the Occurrence of Haplotype Segments in Particular...

help.opticont: Displays Available Objective Functions and Constraints for...

help.opticont4mb: Displays Available Objective Functions and Constraints for...

Kin: A list of class kinMatrices containing kinship matrices

kinlist: Combines Kinship Matrices into a List

kinwac: Calculates Kinships With Age Cohorts

makeA: Calculates the Pedigree-based Additive Relationship Matrix

map: Marker Map for Cattle

noffspring: Calculates Optimum Numbers of Offspring

opticomp: Calculates the Optimum Breed Composition

opticont: Calculates Optimum Contributions of Selection Candidates

opticont4mb: Calculates Optimum Contributions of Selection Candidates...

optiSel-package: Optimum Contribution Selection and Population Genetics

pedBreedComp: Calculates the Pedigree Based Breed Composition of...

pedIBD: Calculates the Pedigree-based Kinship Matrix

pedIBDatN: Calculates the Pedigree Based Kinship at Native Alleles

pedIBDorM: Calculates Kinships taking Allele Origin into Account

PedigWithErrors: Pedigree of Hinterwald cattle

pedInbreeding: Calculates Pedigree Based Inbreeding

pedplot: Plots a Pedigree

Phen: Simulated Phenotypes of Hinterwald Cattle

plot.HaploFreq: Plots Frequencies of Haplotype Segments in Particular Breeds

prePed: *Pre*pares a *Ped*igree

read.indiv: Reads Individual IDs from a Genotype File

segBreedComp: Calculates the Segment Based Breed Composition of Individuals

segIBD: Calculates the Segment Based Kinship Matrix

segIBDandN: Calculates Probabilities that Alleles belong to a Shared...

segIBDatN: Calculates Segment Based Kinship at Native Alleles.

segInbreeding: Calculates Segment Based Inbreeding

segN: Calculates Probabilities of Alleles to belong to Native...

sim2dis: Converts a Similarity Matrix into a Dissimilarity Matrix

subPed: Creates a Subset of a Large Pedigree

summary.kinMatrices: Calculates Genetic Parameters for Age Cohorts

summary.opticont: Summary Statistics and Check of Validity for Optimum...

summary.Pedig: Calculates Summary Statistics for Pedigrees.

Functions

Cattle Man page
Chr1.phased Man page
Chr2.phased Man page
completeness Man page
conttac Man page
ExamplePed Man page
freqlist Man page
genecont Man page
haplofreq Man page
help.opticont Man page
help.opticont4mb Man page
Kin Man page
kinlist Man page
kinwac Man page
makeA Man page
map Man page
noffspring Man page
opticomp Man page
opticont Man page
opticont4mb Man page
optiSel Man page
optiSel-package Man page
pedBreedComp Man page
pedIBD Man page
pedIBDatN Man page
pedIBDorM Man page
PedigWithErrors Man page
pedInbreeding Man page
pedplot Man page
Phen Man page
plot.HaploFreq Man page
prePed Man page
read.indiv Man page
segBreedComp Man page
segIBD Man page
segIBDandN Man page
segIBDatN Man page
segInbreeding Man page
segN Man page
sim2dis Man page
subPed Man page
summary.kinMatrices Man page
summary.opticont Man page
summary.Pedig Man page

Files

inst
inst/extdata
inst/extdata/Chr2.phased
inst/extdata/Chr1.phased
inst/doc
inst/doc/seg-vignette.Rmd
inst/doc/ped-vignette.Rmd
inst/doc/ocs-vignette.html
inst/doc/seg-vignette.R inst/doc/ocs-vignette.R
inst/doc/ocs-vignette.Rmd
inst/doc/ped-vignette.html
inst/doc/seg-vignette.html
inst/doc/ped-vignette.R
src
src/rcpp_genecont.cpp
src/Makevars
src/rcpp_segIBD.cpp
src/rcpp_segIBDandN.cpp
src/rcpp_segInbreeding.cpp
src/rcpp_makeA.cpp
src/rcpp_makeA_lowMem.cpp
src/rcpp_haplofreq.cpp
src/rcpp_segBreedComp.cpp
src/rcpp_completeness.cpp
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/rcpp_nativecont.cpp
src/rcpp_segN.cpp
src/rcpp_segIBDandNVersion2.cpp
NAMESPACE
data
data/PedigWithErrors.rda
data/map.rda
data/ExamplePed.rda
data/Phen.rda
data/Kin.rda
data/Cattle.rda
R
R/opticomp.R R/segInbreeding.R R/getNe.R R/pedBreedComp.R R/pedIBDatN.R R/segIBDatN.R R/segN.R R/summary.opticont.R R/onAttach.R R/freqlist.R R/segBreedComp.R R/genecontALT.R R/pedIBD.R R/help.opticont.R R/pedplot.R R/segIBD.R R/help.opticont4mb.R R/opticont.R R/summary.kinMatrices.R R/read.indiv.R R/opticont4mb.R R/kinlist.R R/RcppExports.R R/genecont.R R/kinwac.R R/pedInbreeding.R R/opticontx.R R/getskip.R R/plot.HaploFreq.R R/prePed.R R/pedIBDorM.R R/subPed.R R/sim2dis.R R/noffspring.R R/getcskip.R R/completeness.R R/makeA.R R/summary.Pedig.R R/haplofreq.R R/segIBDandN.R R/conttac.R
vignettes
vignettes/seg-vignette.Rmd
vignettes/ped-vignette.Rmd
vignettes/ocs-vignette.Rmd
vignettes/HaplotypeEval
vignettes/HaplotypeEval/freq.Angler.Chr1.in.others.txt
vignettes/HaplotypeEval/freq.Angler.Chr2.in.others.txt
vignettes/HaplotypeEval/match.Angler.Chr2.in.others.txt
vignettes/HaplotypeEval/match.Angler.Chr1.in.others.txt
vignettes/references.bib
MD5
build
build/vignette.rds
build/partial.rdb
DESCRIPTION
man
man/pedBreedComp.Rd man/subPed.Rd man/kinlist.Rd man/map.Rd man/opticont.Rd man/makeA.Rd man/noffspring.Rd man/pedIBDorM.Rd man/Chr2.phased.Rd man/segIBDatN.Rd man/genecont.Rd man/Chr1.phased.Rd man/Cattle.Rd man/plot.HaploFreq.Rd man/segIBDandN.Rd man/optiSel-package.Rd man/pedIBD.Rd man/Phen.Rd man/help.opticont4mb.Rd man/PedigWithErrors.Rd man/segBreedComp.Rd man/opticomp.Rd man/freqlist.Rd man/segInbreeding.Rd man/pedIBDatN.Rd man/prePed.Rd man/summary.opticont.Rd man/ExamplePed.Rd man/segN.Rd man/Kin.Rd man/conttac.Rd man/read.indiv.Rd man/sim2dis.Rd man/completeness.Rd man/haplofreq.Rd man/segIBD.Rd man/pedplot.Rd man/help.opticont.Rd man/pedInbreeding.Rd man/summary.Pedig.Rd man/summary.kinMatrices.Rd man/opticont4mb.Rd man/kinwac.Rd

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.