createPop: Create population object from genotype data.frame
In KosukeHamazaki/myBreedSimulatR: R Breeding Simulator for K.Hamazaki

createPop

R Documentation

Create population object from genotype data.frame

Description

Create population object from genotype data.frame

Usage

createPop(
  geno = NULL,
  haplo = NULL,
  lociInfo,
  traitInfo = NULL,
  founderIsInitPop = FALSE,
  seedSimHaplo = NA,
  seedSimRM = NA,
  seedSimMC = NA,
  indNames = NULL,
  popName = NULL,
  verbose = TRUE
)

Arguments

`geno`	[data.frame / matrix] genotype of the individuals encoded in allele dose. If you use real data, you must specify 'geno' or 'haplo' argument.
`haplo`	[array] haplotype of the individuals scored with 0 and 1 (3-dimensional array).
`lociInfo`	[lociInfo object] information about the individuals haplotypes' SNPs (see:lociInfo)
`traitInfo`	[traitInfo class] Specific information of traits (see:traitInfo)
`founderIsInitPop`	[logical] Founder haplotype will be regarded as first population or not.
`seedSimHaplo`	[numeric] Random seed for selecting haplotype from founder haplotype
`seedSimRM`	[numeric] Random seed for mate pairs
`seedSimMC`	[numeric] Random seed for make crosses
`indNames`	[character] NULL or character string vector specifying the individuals names. If NULL, `rownames(geno)` will be used.
`popName`	[character] population's name.
`verbose`	[logical] display information

Value

population object (see:population)

Examples

### create simulation information
mySimInfo <- simInfo$new(simName = "Simulation Example",
                         simGeno = TRUE,
                         simPheno = TRUE,
                         nSimGeno = 1,
                         nSimPheno = 3,
                         nCoreMax = 4,
                         nCorePerGeno = 1,
                         nCorePerPheno = 3,
                         saveDataFileName = NULL)
### create specie information
mySpec <- specie$new(nChr = 3,
                     lChr = c(100, 150, 200),
                     specName = "Example 1",
                     ploidy = 2,
                     mutRate = 10^-8,
                     recombRate = 10^-6,
                     chrNames = c("C1", "C2", "C3"),
                     nLoci = 100,
                     recombRateOneVal = FALSE,
                     effPopSize = 100,
                     simInfo = mySimInfo,
                     verbose = TRUE)
### create lociInfo object
myLoci <- lociInfo$new(genoMap = NULL, specie = mySpec)
plot(myLoci, alpha = 0.1)
### create traitInfo object
myTrait <- traitInfo$new(lociInfo = myLoci,
                         nMarkers = 80,
                         nTraits = 3,
                         nQTLs = c(4, 8, 3),
                         actionTypeEpiSimple = TRUE,
                         qtlOverlap = TRUE,
                         nOverlap = c(2, 3, 0),
                         effCor = 0.1,
                         propDomi = 0.2,
                         interactionMean = c(4, 1, 2))
plot(myTrait)
### create simulated population
simulatedPop <- createPop(geno = NULL,
                          haplo = NULL,
                          lociInfo = myLoci,
                          traitInfo = myTrait,
                          founderIsInitPop = TRUE,
                          popName = "First Population",
                          verbose = FALSE)
simulatedPop$plot(plotTarget = "trueGV",
                  plotType = "violin")
simulatedPop$plot(plotTarget = "trueGV",
                  plotType = "scatter",
                  scatterAxes = 1:3)

KosukeHamazaki/myBreedSimulatR documentation built on Aug. 31, 2024, 3:55 p.m.