Breeding Program Simulations


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Documentation for package ‘AlphaSimR’ version 1.3.1

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A B C D E F G H I L M N P Q R S T U V W misc

-- A --

aa Additive-by-additive epistatic deviations
addSegSite Add segregating site to MapPop
attrition Lose individuals at random

-- B --

bv Breeding value

-- C --

c-method Hybrid population
c-method Raw population with genetic map
c-method Mega-Population
c-method Raw population with genetic map and id
c-method Population
c-method Raw Population
calcGCA Calculate GCA
cChr Combine MapPop chromosomes

-- D --

dd Dominance deviations
doubleGenome Double the ploidy of individuals

-- E --

ebv Estimated breeding value
editGenome Edit genome
editGenomeTopQtl Edit genome - the top QTL

-- F --

fastRRBLUP Fast RR-BLUP

-- G --

genicVarA Additive genic variance
genicVarAA Additive-by-additive genic variance
genicVarD Dominance genic variance
genicVarG Total genic variance
genParam Sumarize genetic parameters
getGenMap Get genetic map
getMisc Get miscelaneous information in a population
getNumThreads Number of available threads
getPed Get pedigree
getQtlMap Get QTL genetic map
getSnpMap Get SNP genetic map
gv Genetic value

-- H --

hybridCross Hybrid crossing
HybridPop-class Hybrid population

-- I --

importGenMap Import genetic map
importHaplo Import haplotypes
importInbredGeno Import inbred, diploid genotypes
isFemale Test if individuals of a population are female or male
isHybridPop Hybrid population
isMale Test if individuals of a population are female or male
isMapPop Raw population with genetic map
isMegaPop Mega-Population
isNamedMapPop Raw population with genetic map and id
isPop Test if object is of a Population class
isRawPop Raw Population

-- L --

LociMap-class Loci metadata

-- M --

makeCross Make designed crosses
makeCross2 Make designed crosses
makeDH Generates DH lines
MapPop-class Raw population with genetic map
meanG Mean genetic values
meanP Mean phenotypic values
MegaPop-class Mega-Population
mergeGenome Combine genomes of individuals
mergePops Merge list of populations
mutate Add Random Mutations

-- N --

NamedMapPop-class Raw population with genetic map and id
newEmptyPop Creates an empty population
newMapPop New MapPop
newMegaPop Create new Mega Population
newPop Create new population
nInd Number of individuals

-- P --

pedigreeCross Pedigree cross
pheno Phenotype
Pop-class Population
popVar Population variance
pullIbdHaplo Pull IBD haplotypes
pullMarkerGeno Pull marker genotypes
pullMarkerHaplo Pull marker haplotypes
pullQtlGeno Pull QTL genotypes
pullQtlHaplo Pull QTL haplotypes
pullSegSiteGeno Pull segregating site genotypes
pullSegSiteHaplo Pull seg site haplotypes
pullSnpGeno Pull SNP genotypes
pullSnpHaplo Pull SNP haplotypes

-- Q --

quickHaplo Quick founder haplotype simulation

-- R --

randCross Make random crosses
randCross2 Make random crosses
RawPop-class Raw Population
reduceGenome Create individuals with reduced ploidy
resetPop Reset population
RRBLUP RR-BLUP Model
RRBLUP2 RR-BLUP Model 2
RRBLUPMemUse RRBLUP Memory Usage
RRBLUP_D RR-BLUP Model with Dominance
RRBLUP_D2 RR-BLUP with Dominance Model 2
RRBLUP_GCA RR-BLUP GCA Model
RRBLUP_GCA2 RR-BLUP GCA Model 2
RRBLUP_SCA RR-BLUP SCA Model
RRBLUP_SCA2 RR-BLUP SCA Model 2
RRsol-class RR-BLUP Solution
runMacs Create founder haplotypes using MaCS
runMacs2 Alternative wrapper for MaCS

-- S --

sampleHaplo Sample haplotypes from a MapPop
selectCross Select and randomly cross
selectFam Select families
selectInd Select individuals
selectOP Select open pollinating plants
selectWithinFam Select individuals within families
self Self individuals
selIndex Selection index
selInt Selection intensity
setEBV Set EBV
setMarkerHaplo Set marker haplotypes
setMisc Set miscelaneous information in a population
setPheno Set phenotypes
setPhenoGCA Set GCA as phenotype
setPhenoProgTest Set progeny test as phenotype
show-method Population
show-method Raw Population
SimParam Simulation parameters
smithHazel Calculate Smith-Hazel weights
solveMKM Solve Multikernel Model
solveMVM Solve Multivariate Model
solveRRBLUP Solve RR-BLUP
solveRRBLUPMK Solve Multikernel RR-BLUP
solveRRBLUPMV Solve Multivariate RR-BLUP
solveRRBLUP_EM Solve RR-BLUP with EM
solveRRBLUP_EM2 Solve RR-BLUP with EM and 2 random effects
solveRRBLUP_EM3 Solve RR-BLUP with EM and 3 random effects
solveUVM Solve Univariate Model

-- T --

TraitA-class Additive trait
TraitA2-class Sex specific additive trait
TraitA2D-class Sex specific additive and dominance trait
TraitAD-class Additive and dominance trait
TraitADE-class Additive, dominance, and epistatic trait
TraitADEG-class Additive, dominance, epistasis, and GxE trait
TraitADG-class Additive, dominance and GxE trait
TraitAE-class Additive and epistatic trait
TraitAEG-class Additive, epistasis and GxE trait
TraitAG-class Additive and GxE trait
transMat Linear transformation matrix

-- U --

usefulness Usefulness criterion

-- V --

varA Additive variance
varAA Additive-by-additive epistatic variance
varD Dominance variance
varG Total genetic variance
varP Phenotypic variance

-- W --

writePlink Writes a Pop-class as PLINK files
writeRecords Write data records

-- misc --

.newPop Create new population (internal)
[-method Hybrid population
[-method Raw population with genetic map
[-method Mega-Population
[-method Raw population with genetic map and id
[-method Population
[-method Raw Population
[[-method Mega-Population