Man pages for neyhartj/pbsim
Simulations of Plant Breeding Experiments
| calc_allele_freq | Calculate the allele frequencies of loci |
| calc_exp_genvar | Calculate the expected genetic variance in simulated families |
| calc_genoval | Hidden functions; generally not to be called by the user |
| calc_haplotype_freq | Calculate the frequency of haplotypes |
| calc_LD | Calculate linkage disequilibrium between loci |
| check_geno | Check a matrix of genotypes for completeness |
| chrlen | Extract the length of chromosomes |
| chrnames | Extract chromosome names |
| combine_pop | Combine a list of populations |
| create_pop | Create a population object |
| find_markerpos | Find the position of markers in the genome |
| find_proxmarkers | Find the position of markers near a locus |
| geno_to_popvar | Convert data for use in PopVar |
| genotype | Genotype a population |
| indnames | Names of individuals |
| induce_dh | Generate doubled-hapoids from crossover data |
| is_haploid | Haploid genotype data |
| map_to_table | Convert the genetic map in the genome to a table |
| markernames | Extract marker names |
| nchr | Extract the number of chromosomes in the genome |
| nind | Number of individuals in a population |
| nloci | Extract the total number of loci in the genome |
| nmar | Extract the number of markers in the genome |
| nqtl | Extract the number of QTL in the genome |
| pheno | Extract values from a population |
| pred_geno_val | Predict genotypic values using genomewide markers |
| pred_genvar | Predict the genetic variance in prospective crosses |
| pred_mar_eff | Predict marker effects in a training population |
| pull_genotype | Pull the genotype data for a named locus |
| pull_plei_qtl | Extract the pleiotropic QTL from the genome |
| pull_qtl | Extract the QTL from a genome |
| qtlnames | Extract the names of QTL in the genome |
| select_pop | Make selections from a population |
| sim_crossing_block | Create a crossing block from a vector of parents |
| sim_family | Simulate a family from a pedigree |
| sim_family_cb | Simulate multiple families from a crossing block |
| sim_founders | Simulate founders |
| sim_gen_model | Define the genetic model of a trait |
| sim_genome | Create a simulated genome |
| sim_multi_gen_model | Define a genetic model for two or more traits |
| sim_pedigree | Create a pedigree for a cross |
| sim_phenoval | Simulate phenotypic values |
| sim_pop | Simulate a population |
| sim_trial | Simulate an experimental field trial |
| split_geno | Split a genotype matrix into chromosomes |
| split_haploid | Split a haploid array into chromosomes |
| subset_pop | Subset a population object for specific individuals |
| summary.genome | Summarize a genome object |
| table_to_map | Convert a table of genetic positions to a map |
