Man pages for MoBPS
Modular Breeding Program Simulator

add.diagAdd something to the diagonal
alpha_to_betaMoore-Penrose-Transfomration
analyze.bvAnalyze genomic values
analyze.populationAnalyze allele frequency of a single marker
bit.snpsDecoding of bitwise-storing in R
bit.storingBitwise-storing in R
breeding.diploidBreeding function
breeding.internInternal function to simulate one meiosis
bv.developmentDevolopment of genetic/breeding value
bv.development.boxDevolopment of genetic/breeding value
bv.standardizationBV standardization
calculate.bvCalculate breeding values
cattle_chipCattle chip
chicken_chipchicken chip
clean.upClean-up recombination points
codeOriginsROrigins-coding(R)
compute.costsCompute costs of a breeding program
compute.costs.cohortsCompute costs of a breeding program
compute.snpsCompute genotype/haplotype
compute.snps_singleCompute genotype/haplotype in gene editing application
creating.diploidGeneration of the starting population
creating.phenotypic.transformCalculate breeding values
creating.traitGeneration of genomic traits
decodeOriginsROrigins-Decoding(R)
derive.loop.elementsDerive loop elements
edges.fromtogen/database/cohorts conversion
edit_animalInternal gene editing function
effect.estimate.addEstimation of marker effects
ensembl.mapEnsemble Map
epiMartini-Test function
ex_jsonex_json
ex_popex_pop
find.chromoPosition detection
find.snpbeforePosition detection
generation.individualFunction to generate a new individual
get.age.pointDerive age point
get.bvExport underlying true breeding values
get.bveExport estimated breeding values
get.classDerive class
get.cohortsExport Cohort-names
get.creating.typeDerive creating type
get.cullingtimeDerive time of culling
get.databasegen/database/cohorts conversion
get.death.pointDerive death point
get.genoDerive genotypes of selected individuals
get.genotypedDerive genotyping status
get.haploDerive haplotypes of selected individuals
get.idDerive class
get.individual.locExport location of individuals from the population list
get.infosExtract bv/pheno/geno of selected individuals
get.mapMap generation
get.pcaDerive class
get.pedigreeDerive pedigree
get.pedigree2Derive pedigree including grandparents
get.pedigree3Derive pedigree parents and grandparents
get.pedmapGenerate plink-file (pedmap)
get.phenoExport underlying phenotypes
get.pheno.offExport underlying phenotypes
get.pheno.off.countExport underlying phenotypes
get.recombiDerive genetic origins
get.reliabilitiesExport underlying reliabilities
get.selectionindexExport underlying selection index
get.time.pointDerive time point
get.vcfGenerate vcf-file
insert.bveExport estimated breeding values
json.simulationGeneration of the starting population
kinship.developmentDevolopment of genetic/breeding value
kinship.empEmpirical kinship
kinship.emp.fastEmpirical kinship
kinship.exp.storeDerive expected kinship
ld.decayGenerate LD plot
maize_chipmaize chip
miesenberger.indexMiesenberger Index
mutation.introMutation intro
new.base.generationSet new base generation
OGCOptimal genetic contribution
pedmap.to.phasedbeaglevcfPerform imputing/phasing
pig_chippig chip
sheep_chipsheep chip
sortdApply sort and unique
ssGBLUPSingle Step GBLUP
summary.populationSummary Population
vlistDerive class
MoBPS documentation built on March 31, 2020, 5:22 p.m.