Breeding Program Simulations


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Documentation for package ‘AlphaSimR’ version 0.13.0

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

-- A --

aa Additive-by-additive epistatic deviations

-- 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
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
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
mergeGenome Combine genomes of individuals
mergePops Merge list of populations
mutate Add Random Mutations

-- 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
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
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
setPheno Set phenotypes
setPhenoGCA Set GCA as phenotype
show-method Population
show-method Raw Population
SimParam Simulation parameters
smithHazel Calculate Smith-Hazel weights

-- 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

-- 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