advance.family | Advance a family |
advance.population | Advance a population |
CAP.haploids | CAP genotypic data in haploid matrix format |
CAP.hmp | CAP genotypic data in rrBLUP encoding |
CAP.lines | The names of the CAP lines |
CAP.markers | Marker information |
design.M | M matrix |
find.pos | Finds the whole genome positions of QTL and markers |
genotype.loci | Genotype loci |
genotypic.value | Calculate the genotypic value of individuals |
invert.mat | Hidden functions |
is.polymorphic | Determine if a locus is polymorphic |
make.contrast | Make a matrix of contrasts |
make.crossing.block | Create a crossing block from known parents |
make.family | Make a family |
make.genome | Make a genome |
make.population | Make a population |
make.predictions | Make genomic predictions |
measure.af | Calculate allele frequencies |
measure.expected.het | Measure expected heterozygosity |
measure.LD | Calculate linkage disequilibrium |
nv_df | Parse results to data.frame |
optimize.subset | Optimize PEVmean or CDmean |
parse.results | Parse the results of the simulation |
PEVmean | PEVmean |
phenotype.population | Generate phenotypic values |
plotting_data | Results |
qtl.eff | Retrieve QTL effects from a genome |
recombine | Simulate recombination |
round.limit | Round with a limit |
select.haploids | Subset the haploid genotypes matrix |
select.population | Apply selection on a population |
select.values | Subset phenotypic or genotypic values |
sim.summarize | Summarize a results data frame |
trait.architecture | Define the trait architecture |
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