Haplotype-Based Tracking of Admixed Population for Breed
Composition Estimation
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Documentation for package ‘HAPTRACE’ version 0.1.1
Help Pages
| Admixplot | Plot for True Breed Composition |
| AlleleFreq | Calculate Allele Frequency |
| BreedEff_Haplo | True Breeding Value (TBV) estimation according to breed of origin |
| BreedPopCross | Function for crossing two population with breed effects according to breed of origin |
| BreedPopSelect | Selecting Population with breed effect according to breed of origin |
| CalQTLeffect | Calculate QTL effect from file generated from ReadQTL (For QMSim generated files) |
| Coded_to_Haplo | Recode Coded haplotypes according to breed of origin into 0 and 1 format |
| DamSample | Select Dams |
| Ext_Pheno | Extract TBV and Phenotype |
| GenBreedPop | Generate Population with specific breed effect |
| generateHP | Generate Historical Population |
| generateMAP | Generate MAP file |
| GenOnePopulation | Simulate Population |
| MakeGeno | Make Genotype from Haplotype |
| mapQTLfile | Create combined map and qtl file |
| MatingPop | Function for mating sire and dam |
| MutationRate | Adding Mutation |
| Ped_Pheno | Combine Pedigree and Phenotype data |
| plinkped | Generate PLINK pedigree file |
| plotHaplo | Plot for Haplotype segments |
| PopSelect | Selecting Population with selection criteria random, phenotype and true breeding value |
| PopulationID | Adding Population Code before simulating the population |
| QMSim_PlinkMAP | Format PLINK MAP file from QMSim |
| QTLeffects | Calculation QTL effects |
| QTL_densityplot | Plot for the QTL effect |
| Random_gametes | Random selection of sire and dam gametes |
| ReadQTL | Read QTL file obtained from QMSim |
| read_qmsim_geno | Read QMSim Marker/QTL Genotype File |
| Recode_Haplotype | Recode Haplotype with different breed codes |
| RecombinationPoint | Add Recombination |
| recProbplot | Plot for recombination points and recombination probability |
| Reformat_BLUPF90 | Reformat genotype data for BLUPF90 analysis |
| Rescale | Rescaling SNP Effect |
| SireSample | Select Sires |
| TBV_Haplo | Calculation of True breeding Value (TBV) |
| trueBreedComp | Calculate True Breed Proportion with coded haplotype |
| TwoPopCross | Function for crossing two populations |
| Var_PhenoRecords | Generate variance components and phenotypic records |