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

advance.familyAdvance a family
advance.populationAdvance a population
CAP.haploidsCAP genotypic data in haploid matrix format
CAP.hmpCAP genotypic data in rrBLUP encoding
CAP.linesThe names of the CAP lines
CAP.markersMarker information
design.MM matrix
find.posFinds the whole genome positions of QTL and markers
genotype.lociGenotype loci
genotypic.valueCalculate the genotypic value of individuals
invert.matHidden functions
is.polymorphicDetermine if a locus is polymorphic
make.contrastMake a matrix of contrasts
make.crossing.blockCreate a crossing block from known parents
make.familyMake a family
make.genomeMake a genome
make.populationMake a population
make.predictionsMake genomic predictions
measure.afCalculate allele frequencies
measure.expected.hetMeasure expected heterozygosity
measure.LDCalculate linkage disequilibrium
nv_dfParse results to data.frame
optimize.subsetOptimize PEVmean or CDmean
parse.resultsParse the results of the simulation
PEVmeanPEVmean
phenotype.populationGenerate phenotypic values
plotting_dataResults
qtl.effRetrieve QTL effects from a genome
recombineSimulate recombination
round.limitRound with a limit
select.haploidsSubset the haploid genotypes matrix
select.populationApply selection on a population
select.valuesSubset phenotypic or genotypic values
sim.summarizeSummarize a results data frame
trait.architectureDefine the trait architecture
UMN-BarleyOatSilphium/GSSimTPUpdate documentation built on June 3, 2017, 6:42 a.m.