Proceed several crosses

Usage

makeCrosses(crosses, pop)

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

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)
rawHaplo3 <- matrix(sample(c(0, 1), (3 + 4 + 5) * 2, replace = TRUE),
                    nrow = 2)
colnames(rawHaplo3) <- sprintf(fmt = paste0("SNP%0", 2,"i"),
                              1:(3 + 4 + 5))
haplo3 <- haplotype$new(SNPinfo = SNPs,
                       haplo = rawHaplo3)


# 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)
myInd3 <-  individual$new(name = "Ind 3",
                         specie = mySpec,
                         parent1 = "OkaaSan",
                         parent2 = "OtouSan",
                         haplo = haplo3,
                         verbose = FALSE)
myPop <- population$new(name = "My Population 1",
                        inds = list(myInd1, myInd2, myInd3),
                        verbose = FALSE)

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

makeCrosses(crossToDo, myPop)
#> $`Off 1-2`
#> <individual>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     generateGametes: function (n = 1) 
#>     haplo: Haplotype, R6
#>     initialize: function (name = "Unnamed", specie = specie$new(), parent1 = NA, 
#>     name: Off 1-2
#>     parent1: Ind 1
#>     parent2: Ind 2
#>     specie: Specie, R6
#>   Private:
#>     checkHaplo: function () 
#> 
#> $`Off 1-3`
#> <individual>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     generateGametes: function (n = 1) 
#>     haplo: Haplotype, R6
#>     initialize: function (name = "Unnamed", specie = specie$new(), parent1 = NA, 
#>     name: Off 1-3
#>     parent1: Ind 1
#>     parent2: Ind 3
#>     specie: Specie, R6
#>   Private:
#>     checkHaplo: function () 
#> 
#> $`Off 2-3`
#> <individual>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     generateGametes: function (n = 1) 
#>     haplo: Haplotype, R6
#>     initialize: function (name = "Unnamed", specie = specie$new(), parent1 = NA, 
#>     name: Off 2-3
#>     parent1: Ind 2
#>     parent2: Ind 3
#>     specie: Specie, R6
#>   Private:
#>     checkHaplo: function () 
#>