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MoBPS (version 1.6.64)

Modular Breeding Program Simulator

Description

Framework for the simulation framework for the simulation of complex breeding programs and compare their economic and genetic impact. The package is also used as the background simulator for our a web-based interface . Associated publication: Pook et al. (2020) .

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Version

Install

install.packages('MoBPS')

Monthly Downloads

196

Version

1.6.64

License

GPL (>= 3)

Maintainer

Torsten Pook

Last Published

November 9th, 2021

Functions in MoBPS (1.6.64)

codeOriginsR

Origins-coding(R)
add.combi

Add a trait as a linear combination of other traits
chicken_chip

chicken chip
add.diag

Add something to the diagonal
generation.individual

Function to generate a new individual
get.dendrogram

Dendrogram
bit.snps

Decoding of bitwise-storing in R
bit.storing

Bitwise-storing in R
get.dendrogram.heatmap

Dendrogram Heatmap
demiraculix

Remove miraculix-coding for genotypes
find.chromo

Position detection (chromosome)
decodeOriginsR

Origins-Decoding(R)
clean.up

Clean-up recombination points
creating.trait

Generation of genomic traits
get.database

gen/database/cohorts conversion
find.snpbefore

Position detection (SNPs)
derive.loop.elements

Derive loop elements
get.npheno

Export underlying number of observations per phenotype
get.pca

Principle components analysis
get.death.point

Derive death point
get.time.point

Derive time point
get.individual.loc

Export location of individuals from the population list
get.pedigree2

Derive pedigree including grandparents
get.pedigree

Derive pedigree
get.id

Derive ID on an individual
kinship.development

Devolopment of genetic/breeding value
kinship.emp

Empirical kinship
get.selectionindex

Export underlying last used selection index
breeding.diploid

Breeding function
analyze.bv

Analyze genomic values
check.parents

Relatedness check between two individuals
alpha_to_beta

Moore-Penrose-Transfomration
cattle_chip

Cattle chip
add.founder.kinship

Add a relationship matrix for founder individuals
plot.population

Plot Population
creating.diploid

Generation of the starting population
pig_chip

pig chip
breeding.intern

Internal function to simulate one meiosis
get.pheno

Export underlying phenotypes
creating.phenotypic.transform

Create a phenotypic transformation
insert.bve

Manually enter estimated breeding values
get.pheno.off

Export underlying offspring phenotypes
json.simulation

Simulation of a breeding program based on a JSON-file from MoBPSweb
OGC

Optimal genetic contribution
maize_chip

maize chip
ld.decay

Generate LD plot
add.array

Add a genotyping array
bv.development.box

Development of genetic/breeding value using a boxplot
bv.development

Development of genetic/breeding value
ex_json

ex_json
edit_animal

Internal gene editing function
effect.estimate.add

Estimation of marker effects
vlist

Generation of a sublist
set.class

Export estimated breeding values
set.default

Set defaults
compute.snps

Compute genotype/haplotype
get.class

Derive class
ex_pop

ex_pop
analyze.population

Analyze allele frequency of a single marker
get.genotyped.snp

Derive which markers are genotyped of selected individuals
get.effective.size

Estimate effective population size
calculate.bv

Calculate breeding values
get.effect.freq

Compute marker frequency in QTL-markers
bv.standardization

BV standardization
get.cohorts

Export Cohort-names
compute.snps_single

Compute genotype/haplotype in gene editing application
get.infos

Extract bv/pheno/geno of selected individuals
get.pedmap

Generate plink-file (pedmap)
get.pedigree3

Derive pedigree parents and grandparents
get.map

Map generation
effective.size

Estimate effective population size
compute.costs

Compute costs of a breeding program
get.bv

Export underlying true breeding values
compute.costs.cohorts

Compute costs of a breeding program by cohorts
get.qtl.variance

QTL effect variance extraction
get.bve

Export estimated breeding values
get.haplo

Derive haplotypes of selected individuals
get.phylogenetic.tree

Phylogenetic Tree
miesenberger.index

Miesenberger Index
get.pheno.off.count

Export underlying number of used offspring for offspring phenotypes
miraculix

Add miraculix-coding for genotypes
epi

Martini-Test function
get.admixture

Admixture Plot
get.age.point

Derive age point
sortd

Apply sort and unique
sheep_chip

sheep chip
mutation.intro

Mutation intro
new.base.generation

Set new base generation
get.recombi

Derive genetic origins
ssGBLUP

Single Step GBLUP
summary.population

Summary Population
get.distance

Calculate Nei distance between two or more population
get.dendrogram.trait

Dendrogram
get.creating.type

Derive creating type
get.cullingtime

Derive time of culling
get.qtl

QTL extraction
get.genotyped

Derive genotyping status
get.qtl.effects

QTL effect extraction
get.geno

Derive genotypes of selected individuals
get.reliabilities

Export underlying reliabilities
get.vcf

Generate vcf-file
group.diff

Function to exclude individuals from a database
get.selectionbve

Export derived breeding values based on the selection index
pedmap.to.phasedbeaglevcf

Internal function to perform imputing/phasing
kinship.exp

Derive expected kinship
kinship.emp.fast

Approximate empirical kinship
pedigree.simulation

Simulation of a given pedigree
combine.traits

Combine traits
diag.mobps

Add a genotyping array
founder.simulation

Founder simulation
edges.fromto

Detection of parental/child nodes