# Modular Breeding Program Simulator

## Documentation for package ‘MoBPS’ version 1.6.64

- DESCRIPTION file.

## Help Pages

A B C D E F G I J K L M N O P S V

## -- A --

add.array | Add a genotyping array
add.combi | Add a trait as a linear combination of other traits
add.diag | Add something to the diagonal
add.founder.kinship | Add a relationship matrix for founder individuals
alpha_to_beta | Moore-Penrose-Transfomration
analyze.bv | Analyze genomic values
analyze.population | Analyze allele frequency of a single marker

## -- B --

bit.snps | Decoding of bitwise-storing in R
bit.storing | Bitwise-storing in R
breeding.diploid | Breeding function
breeding.intern | Internal function to simulate one meiosis
bv.development | Development of genetic/breeding value
bv.development.box | Development of genetic/breeding value using a boxplot
bv.standardization | BV standardization

## -- C --

calculate.bv | Calculate breeding values
cattle_chip | Cattle chip
check.parents | Relatedness check between two individuals
chicken_chip | chicken chip
clean.up | Clean-up recombination points
codeOriginsR | Origins-coding(R)
combine.traits | Combine traits
compute.costs | Compute costs of a breeding program
compute.costs.cohorts | Compute costs of a breeding program by cohorts
compute.snps | Compute genotype/haplotype
compute.snps_single | Compute genotype/haplotype in gene editing application
creating.diploid | Generation of the starting population
creating.phenotypic.transform | Create a phenotypic transformation
creating.trait | Generation of genomic traits

## -- D --

decodeOriginsR | Origins-Decoding(R)
demiraculix | Remove miraculix-coding for genotypes
derive.loop.elements | Derive loop elements
diag.mobps | Add a genotyping array

## -- E --

edges.fromto | Detection of parental/child nodes
edit_animal | Internal gene editing function
effect.estimate.add | Estimation of marker effects
effective.size | Estimate effective population size
epi | Martini-Test function
ex_json | ex_json
ex_pop | ex_pop

## -- F --

find.chromo | Position detection (chromosome)
find.snpbefore | Position detection (SNPs)
founder.simulation | Founder simulation

## -- G --

generation.individual | Function to generate a new individual
get.admixture | Admixture Plot
get.age.point | Derive age point
get.bv | Export underlying true breeding values
get.bve | Export estimated breeding values
get.class | Derive class
get.cohorts | Export Cohort-names
get.creating.type | Derive creating type
get.cullingtime | Derive time of culling
get.database | gen/database/cohorts conversion
get.death.point | Derive death point
get.dendrogram | Dendrogram
get.dendrogram.heatmap | Dendrogram Heatmap
get.dendrogram.trait | Dendrogram
get.distance | Calculate Nei distance between two or more population
get.effect.freq | Compute marker frequency in QTL-markers
get.effective.size | Estimate effective population size
get.geno | Derive genotypes of selected individuals
get.genotyped | Derive genotyping status
get.genotyped.snp | Derive which markers are genotyped of selected individuals
get.haplo | Derive haplotypes of selected individuals
get.id | Derive ID on an individual
get.individual.loc | Export location of individuals from the population list
get.infos | Extract bv/pheno/geno of selected individuals
get.map | Map generation
get.npheno | Export underlying number of observations per phenotype
get.pca | Principle components analysis
get.pedigree | Derive pedigree
get.pedigree2 | Derive pedigree including grandparents
get.pedigree3 | Derive pedigree parents and grandparents
get.pedmap | Generate plink-file (pedmap)
get.pheno | Export underlying phenotypes
get.pheno.off | Export underlying offspring phenotypes
get.pheno.off.count | Export underlying number of used offspring for offspring phenotypes
get.phylogenetic.tree | Phylogenetic Tree
get.qtl | QTL extraction
get.qtl.effects | QTL effect extraction
get.qtl.variance | QTL effect variance extraction
get.recombi | Derive genetic origins
get.reliabilities | Export underlying reliabilities
get.selectionbve | Export derived breeding values based on the selection index
get.selectionindex | Export underlying last used selection index
get.time.point | Derive time point
get.vcf | Generate vcf-file
group.diff | Function to exclude individuals from a database

## -- I --

insert.bve | Manually enter estimated breeding values

## -- J --

json.simulation | Simulation of a breeding program based on a JSON-file from MoBPSweb

## -- K --

kinship.development | Devolopment of genetic/breeding value
kinship.emp | Empirical kinship
kinship.emp.fast | Approximate empirical kinship
kinship.exp | Derive expected kinship

## -- L --

ld.decay | Generate LD plot

## -- M --

maize_chip | maize chip
miesenberger.index | Miesenberger Index
miraculix | Add miraculix-coding for genotypes
mutation.intro | Mutation intro

## -- N --

new.base.generation | Set new base generation

## -- O --

OGC | Optimal genetic contribution

## -- P --

pedigree.simulation | Simulation of a given pedigree
pedmap.to.phasedbeaglevcf | Internal function to perform imputing/phasing
pig_chip | pig chip
plot.population | Plot Population

## -- S --

set.class | Export estimated breeding values
set.default | Set defaults
sheep_chip | sheep chip
sortd | Apply sort and unique
ssGBLUP | Single Step GBLUP
summary.population | Summary Population

## -- V --

vlist | Generation of a sublist