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 |
aa | Additive-by-additive epistatic deviations |
AlphaSimR | AlphaSimR: Breeding Program Simulations |
bv | Breeding value |
c-method | Hybrid population |
c-method | Raw population with genetic map |
c-method | Population |
c-method | Raw Population |
calcGCA | Calculate GCA |
dd | Dominance deviations |
ebv | Estimated breeding value |
editGenome | Edit genome |
editGenomeTopQtl | Edit genome - the top QTL |
fastRRBLUP | Fast RR-BLUP |
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 |
hybridCross | Hybrid crossing |
HybridPop-class | Hybrid population |
LociMap-class | Loci metadata |
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 |
newMapPop | New MapPop |
newPop | Create new Population |
nInd | Number of individuals |
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 |
quickHaplo | Quick founder haplotype simulation |
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 |
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 |
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 |
usefulness | Usefulness criterion |
varA | Additive variance |
varAA | Additive-by-additive epistatic variance |
varD | Dominance variance |
varG | Total genetic variance |
varP | Phenotypic variance |
writePlink | Writes a Pop-class as PLINK files |
writeRecords | Write data records |
[-method | Hybrid population |
[-method | Raw population with genetic map |
[-method | Population |
[-method | Raw Population |