Man pages for UMN-BarleyOatSilphium/GSSimTPUpdate
Code and data to accompany the publication [TITLE]
| 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 |
