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 |
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