Data Simulation for Life Science and Breeding
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Documentation for package ‘simer’ version 0.9.0.4
Help Pages
| annotation | Annotation simulation |
| build.cov | Correlation building |
| cal.eff | QTN genetic effects |
| checkEnv | Environmental factor checking |
| generate.map | Marker information |
| generate.pop | Population generator |
| geno.cvt1 | Genotype code convertor 1 |
| geno.cvt2 | Genotype code convertor 2 |
| genotype | Genotype simulation |
| getfam | Family index and within-family index |
| GxG.network | Genetic interaction network |
| IndPerGen | Individual number per generation |
| logging.initialize | Logging initialization |
| logging.log | Logging |
| logging.print | Logging printer |
| mate | Mate |
| mate.2waycro | Two-way cross |
| mate.3waycro | Three-way cross |
| mate.4waycro | Four-way cross process |
| mate.assort | Assortative mating |
| mate.backcro | Back cross |
| mate.clone | Clone |
| mate.dh | Doubled haploid |
| mate.disassort | Disassortative mating |
| mate.randexself | Random mating excluding self-pollination |
| mate.randmate | Random mating |
| mate.selfpol | Self-pollination |
| mate.userped | User-specified pedigree mating |
| param.annot | Annotation parameters generator |
| param.geno | Genotype parameters generator |
| param.global | Global parameters generator |
| param.pheno | Phenotype parameters generator |
| param.reprod | Reproduction parameters generator |
| param.sel | Selection parameters generator |
| param.simer | Parameter generator |
| phenotype | Phenotype simulation |
| pop.geno | Raw genotype matrix from outside in simdata |
| pop.map | Map file from outside in simdata |
| remove_bigmatrix | Big.matrix removing |
| reproduces | Reproduction |
| selects | Selection |
| simer | Simer |
| simer.Data | Data handling |
| simer.Data.Bfile2MVP | simer.Data.Bfile2MVP: To transform plink binary data to MVP package |
| simer.Data.cHIBLUP | Genetic evaluation |
| simer.Data.Env | Environmental factor selection |
| simer.Data.Geno | Genotype data quality control |
| simer.Data.Impute | Genotype data imputation |
| simer.Data.Json | Data quality control |
| simer.Data.Kin | simer.Data.EMMA: To construct EMMA kinship matrix |
| simer.Data.Map | simer.Data.Map: To check map file |
| simer.Data.MVP2Bfile | simer.Data.MVP2Bfile: To transform MVP data to binary format |
| simer.Data.MVP2MVP | Genotype data conversion |
| simer.Data.Ped | Pedigree data quality control |
| simer.Data.Pheno | Phenotype data quality control |
| simer.Data.SELIND | Selection index construction |
| simer.Version | Simer version |
| write.file | File writing |