Modular Breeding Program Simulator
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Documentation for package ‘MoBPS’ version 1.13.1
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A B C D E F G I J K L M N O P R S V W
-- 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.diversity | Add additional diverse material to a population |
| add.fixed.effects | Add fixed effects to traits |
| 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 |
| breeding.intern1 | Internal function to simulate one meiosis |
| breeding.intern2 | Internal function to simulate one meiosis |
| breeding.intern3 | Internal function to simulate one meiosis |
| breeding.intern4 | Internal function to simulate one meiosis |
| breeding.intern5 | Internal function to simulate one meiosis |
| breeding.intern6 | Internal function to simulate one meiosis |
| breeding.intern7 | Internal function to simulate one meiosis |
| breeding.intern8 | 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 |
| computing.costs | Compute costs of a breeding program |
| computing.costs.cohorts | Compute costs of a breeding program by cohorts |
| computing.snps | Compute genotype/haplotype |
| computing.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 | Diagonal matrix |
-- 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 |
| exist.cohort | Function to extract if a cohort exists |
| 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.allele.freq | Calculate allele frequencies |
| get.bv | Export underlying true breeding values |
| get.bve | Export estimated breeding values |
| get.class | Derive class |
| get.cohorts | Export Cohort-names |
| get.cohorts.individual | Derive ID on an individual |
| get.computing.time | Derive computing time |
| get.creating.type | Derive creating type |
| get.culling.time | Derive culling time |
| get.culling.type | Derive culling 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.fixed.effects.p | Export parametrization of fixed effects |
| get.geno | Derive genotypes of selected individuals |
| get.geno.time | Derive genotyping timepoint |
| 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.index | Putting together indices for GxE / multi trait |
| get.infos | Extract bv/pheno/geno of selected individuals |
| get.is.first | First copy |
| get.is.last | Last copy |
| get.litter | Export litter |
| get.litter.effect | Export litter effect |
| get.maf | Calculate minor allele frequencies |
| get.map | Map generation |
| get.ngen | Number of generations |
| get.nindi | Number of individuals |
| get.npheno | Export underlying number of observations per phenotype |
| get.ntrait | Number of traits |
| get.pca | Principle components analysis |
| get.pedigree | Derive pedigree |
| get.pedigree.visual | Draw pedigree |
| get.pedigree2 | Derive pedigree including grandparents |
| get.pedigree3 | Derive pedigree parents and grandparents |
| get.pedigree_old | Derive pedigree |
| get.pedmap | Generate plink-file (pedmap) |
| get.pen | Export pen ID |
| get.pen.effect | Export pen-effects |
| 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.pheno.single | Export underlying phenotypes |
| get.pheno.time | Derive phenotyping time point |
| get.phylogenetic.tree | Phylogenetic Tree |
| get.plink | Generate binary plink-file |
| get.pool | Export founder pool |
| get.pool.founder | Derive founder pool |
| get.qtl | QTL extraction |
| get.qtl.effects | QTL effect extraction |
| get.qtl.variance | QTL effect variance extraction |
| get.recombi | Derive genetic origins |
| get.reliability | Export underlying reliabilities |
| get.selectionbve | Export derived breeding values based on the selection index |
| get.selectionindex | Export underlying last used selection index |
| get.sex | Extraction of individual sex |
| get.size | Number of individuals in each generation |
| get.snapshot | Derive snapshot of selected individuals |
| get.snapshot.single | Derive snapshot of selected individuals |
| get.time.point | Derive time point of generation |
| get.trafo.p | Export parametrization of fixed effects |
| get.trafo.p.single | Export parametrization of fixed effects |
| get.trait.name | Name of traits |
| get.uhat | Export estimated SNP effects |
| get.variance | Derive variances components (add/dom) |
| get.variance.components | Derive variance components |
| get.vcf | Generate vcf-file |
| group.diff | Exclude individuals from a database |
-- I --
| inbreeding.emp | Empirical kinship |
| inbreeding.exp | Expected inbreeding |
| insert.bv | Manually enter breeding values |
| insert.bve | Manually enter estimated breeding values |
| insert.pheno | Manually enter phenotypes |
| insert.pheno.single | Manually enter phenotypes |
-- J --
| json.simulation | Simulation of a breeding program based on a JSON-file from MoBPSweb |
-- K --
| kinship.development | Development of genetic/breeding value |
| kinship.emp | Empirical kinship |
| kinship.emp.fast | Approximate empirical kinship |
| kinship.emp.fast.between | Approximate empirical kinship |
| kinship.exp | Derive expected kinship |
-- L --
| ld.decay | Generate LD plot |
-- M --
| maize_chip | maize chip |
| matrix.posdef | Projection positive definite |
| merging.cohorts | Merging of cohorts |
| merging.trait | Generation of genomic traits |
| 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 |
| ogc.mobps | Breeding function |
| optimize.cores | Optimize generation cores |
-- P --
| pedigree.matrix | Derive pedigree relationship matrix |
| pedigree.simulation | Simulation of a given pedigree |
| pedmap.to.phasedbeaglevcf | Internal function to perform imputing/phasing |
| pig_chip | pig chip |
| plot.population | Plot Population |
-- R --
| recalculate.bv | Recalculate genomic values |
| recalculate.manual | Recalculate genomic values |
| recombination.function.haldane | Haldane recombination function |
| renaming.cohort | Rename a cohort |
| rowMedian | Row-wise Median |
-- S --
| scaling.relationship | scaling.relationship |
| set.age.point | Set age points |
| set.class | Set class |
| set.default | Set defaults |
| set.mean.pool | Set differences between founder pool |
| set.time.point | Set time point |
| sheep_chip | sheep chip |
| sortd | Apply sort and unique |
| ssGBLUP | Single Step GBLUP |
| summary.population | Summary Population |
-- V --
| vlist | Generation of a sublist |
-- W --
| write.pedigree | write.pedigree.mixblup |