Cross two individuals together

Usage

makeSingleCross(ind1, ind2, names, n = 1, verbose = TRUE)

Arguments

ind1: parent 1
ind2: parent 2
names: names of the descendants
n: number of descendants
verbose: print informations

Value

list of new individuals

Examples

# create specie:
mySpec <- specie$new(nChr = 3,
                     lchr = c(100, 150, 200),
                     lchrCm = 100,
                     verbose = FALSE)

# simulate SNP:
SNPcoord <- data.frame(chr = c(rep("Chr1", 3),
                               rep("Chr2", 4),
                               rep("Chr3", 5)),
                       physPos = c(sample(100, 3),
                               sample(150, 4),
                               sample(200, 5)),
                       linkMapPos = NA,
                       SNPid = sprintf(fmt = paste0("SNP%0", 2,"i"),
                                       1:(3 + 4 + 5)))

# create SNPinfo object:
SNPs <- SNPinfo$new(SNPcoord = SNPcoord, specie = mySpec)


# simulate haplotype:
rawHaplo1 <- matrix(sample(c(0, 1), (3 + 4 + 5) * 2, replace = TRUE),
                    nrow = 2)
colnames(rawHaplo1) <- sprintf(fmt = paste0("SNP%0", 2,"i"),
                              1:(3 + 4 + 5))
haplo1 <- haplotype$new(SNPinfo = SNPs,
                       haplo = rawHaplo1)
rawHaplo2 <- matrix(sample(c(0, 1), (3 + 4 + 5) * 2, replace = TRUE),
                    nrow = 2)
colnames(rawHaplo2) <- sprintf(fmt = paste0("SNP%0", 2,"i"),
                              1:(3 + 4 + 5))
haplo2 <- haplotype$new(SNPinfo = SNPs,
                       haplo = rawHaplo2)


# create individuals:
myInd1 <-  individual$new(name = "Ind 1",
                         specie = mySpec,
                         parent1 = "OkaaSan",
                         parent2 = "OtouSan",
                         haplo = haplo1,
                         verbose = FALSE)
myInd2 <-  individual$new(name = "Ind 2",
                         specie = mySpec,
                         parent1 = "OkaaSan",
                         parent2 = "OtouSan",
                         haplo = haplo2,
                         verbose = FALSE)
offspring <- makeSingleCross(myInd1, myInd2, names = "off 1")
offspring
#> $`off 1`
#> <individual>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     generateGametes: function (n = 1) 
#>     haplo: Haplotype, R6
#>     initialize: function (name = "Unnamed", specie = specie$new(), parent1 = NA, 
#>     name: off 1
#>     parent1: Ind 1
#>     parent2: Ind 2
#>     specie: Specie, R6
#>   Private:
#>     checkHaplo: function () 
#>