Modular Breeding Program Simulator
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Documentation for package ‘MoBPS’ version 1.6.64
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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 |