Breeding Program Simulations


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Documentation for package ‘AlphaSimR’ version 0.10.0

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

AlphaSimR-package AlphaSimR: Breeding Program Simulations

-- A --

aa Additive-by-additive epistatic deviations
AlphaSimR AlphaSimR: Breeding Program Simulations

-- B --

bv Breeding value

-- C --

c-method Hybrid population
c-method Raw population with genetic map
c-method Population
c-method Raw Population
calcGCA Calculate GCA

-- D --

dd Dominance deviations

-- E --

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

-- F --

fastRRBLUP Fast RR-BLUP

-- G --

GCAsol-class RR-BLUP GCA Solution
genicVarA Additive genic variance
genicVarAA Additive-by-additive genic variance
genicVarD Dominance genic variance
genicVarG Total genic variance
genParam Sumarize genetic parameters
getQtlMap Get QTL genetic map
getSnpMap Get SNP genetic map
gv Genetic value

-- H --

hybridCross Hybrid crossing
HybridPop-class Hybrid 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
mergePops Merge list of populations

-- N --

newMapPop New MapPop
newPop Create new Population
nInd Number of individuals

-- P --

pedigreeCross Pedigree cross
pheno Phenotype
Pop-class Population
popVar Population variance
pullIbdHaplo Pull Identity By Descent (IBD) haplotypes
pullMultipleSnpGeno Pull SNP genotype for multiple snp chips
pullMultipleSnpHaplo Pull SNP haplotypes for multiple chips
pullQtlGeno Pull QTL genotype
pullQtlHaplo Pull QTL haplotypes
pullSegSiteGeno Pull seg site genotypes
pullSegSiteHaplo Pull seg site haplotypes
pullSnpGeno Pull SNP genotype
pullSnpHaplo Pull SNP haplotypes

-- Q --

quickHaplo Quick founder haplotype simulation

-- R --

randCross Make random crosses
randCross2 Make random crosses
RawPop-class Raw Population
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
RRDsol-class RR-BLUP Solution with Dominance
RRsol-class RR-BLUP Solution
runMacs Create founder haplotypes using MaCS
runMacs2 Alternative wrapper for MaCS

-- S --

sampleHaplo Sample haplotypes from a MapPop
SCAsol-class RR-BLUP SCA Solution
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
setPheno Set phenotypes
setPhenoGCA Set GCA as phenotype
SimParam Simulation parameters
SimParam_addSnpChip Add SNP chip
SimParam_addStructuredSnpChips Add Structured SNP chips
SimParam_addTraitA Add additive traits
SimParam_addTraitAD Add additive and dominance traits
SimParam_addTraitADE Add additive, dominance and epistasis traits
SimParam_addTraitADEG Add an additive, dominance, and epistasis GxE trait
SimParam_addTraitADG Add an additive and dominance GxE trait
SimParam_addTraitAE Add additive and epistasis traits
SimParam_addTraitAEG Add additive and epistasis GxE traits
SimParam_addTraitAG Add additive GxE traits
SimParam_manAddSnpChip Manually add SNP chip
SimParam_manAddTrait Manually add trait
SimParam_new Create new simulation
SimParam_removeFounderPop Remove founder population
SimParam_removeSnpChip Remove SNP chip
SimParam_removeTrait Remove trait
SimParam_rescaleTraits Rescale traits
SimParam_resetPed Reset pedigree
SimParam_restrSegSites Restrict segregating sites
SimParam_setCorE Set correlated error variance
SimParam_setGender Set gender in simulation
SimParam_setRecRatio Set gender specific recombination
SimParam_setTrackPed Set pedigree tracking
SimParam_setTrackRec Set recombination tracking
SimParam_setVarE Set simulation error variance
SimParam_switchFemaleMap Switch female genetic map
SimParam_switchFounderPop Switch founder population
SimParam_switchGenMap Switch genetic map
SimParam_switchMaleMap Switch male genetic map
SimParam_switchSnpChip Switch SNP chip
SimParam_switchTrait Switch trait
smithHazel Calculate Smith-Hazel weights

-- T --

TraitA-class Additive 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

-- 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 --

[-method Hybrid population
[-method Raw population with genetic map
[-method Population
[-method Raw Population