makeCrosses: Proceed to several crosses

In KosukeHamazaki/myBreedSimulatR: R Breeding Simulator for K.Hamazaki

Proceed to several crosses

Description

Proceed to several crosses

Usage

makeCrosses(crosses, pop, seed = NULL)

Arguments

crosses	data.frame with crossing instructions: parents names ind1 ind2, number of descendant n and names of descendant names
pop	list of individuals containing the parents
seed	Random seed for make crosses

Value

list of new individuals

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 = c(3, 4, 5),
                     recombRateOneVal = FALSE,
                     effPopSize = 3,
                     simInfo = mySimInfo,
                     verbose = TRUE)

### create lociInfo object
myLoci <- lociInfo$new(genoMap = NULL, specie = mySpec)

### simulate haplotype
rawHaplo1 <- matrix(sample(c(0, 1), (3 + 4 + 5) * 2, replace = TRUE),
                    nrow = 2)
colnames(rawHaplo1) <- paste0("Locus_", 1:(3 + 4 + 5))

myHaplo1 <- myBreedSimulatR::haplotype$new(lociInfo = myLoci,
                                           haplo = rawHaplo1)

rawHaplo2 <- matrix(sample(c(0, 1), (3 + 4 + 5) * 2, replace = TRUE),
                    nrow = 2)
colnames(rawHaplo2) <- paste0("Locus_", 1:(3 + 4 + 5))

myHaplo2 <- myBreedSimulatR::haplotype$new(lociInfo = myLoci,
                                           haplo = rawHaplo2)

### create individuals:
myInd1 <-  individual$new(name = "Ind 1",
                          specie = mySpec,
                          parent1 = "OkaaSan1",
                          parent2 = "OtouSan1",
                          haplo = myHaplo1,
                          verbose = TRUE)

myInd2 <-  individual$new(name = "Ind 2",
                          specie = mySpec,
                          parent1 = "OkaaSan2",
                          parent2 = "OtouSan2",
                          haplo = myHaplo2,
                          verbose = TRUE)

myInd3 <-  individual$new(name = "Ind 3",
                          specie = mySpec,
                          parent1 = "OkaaSan1",
                          parent2 = "OtouSan1",
                          haplo = myHaplo1,
                          verbose = TRUE)

### crate population
myPop <- population$new(name = "My Population 1",
                        generation = 1,
                        inds = list(myInd1, myInd2, myInd3),
                        verbose = FALSE)

### make crosses
crossToDo <- data.frame(ind1 = c("Ind 1", "Ind 1", "Ind 2"),
                        ind2 = c("Ind 2", "Ind 3", "Ind 3"),
                        n = c(1, 1, 2),
                        names = c("Off 1-2", "Off 1-3", "Off 2-3"))
makeCrosses(crossToDo, myPop)

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