R/buildSelfingTree.R

In selfingTree: Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing

## Copyright (c) 2014, Pioneer Hi-Bred International, Inc.

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buildSelfingTree <- function(genF,generation,gam1,gam2){
    
    ## F2
    F <- genF(gam1,gam2)

    ## F3
    if(generation > 2){
        for(i in 1:length(F)){
            F[[i]][[3]] <- genF(F[[i]][[1]][1,],F[[i]][[1]][2,])
        }
    }

    ## F4
    if(generation > 3){
        for(i in 1:length(F))
            for(j in 1:length(F[[i]][[3]]))
                F[[i]][[3]][[j]][[3]] <- genF(F[[i]][[3]][[j]][[1]][1,],F[[i]][[3]][[j]][[1]][2,])
    }
    
    ## F5
    if(generation > 4){
        for(i in 1:length(F))
            for(j in 1:length(F[[i]][[3]]))
                for(k in 1:length(F[[i]][[3]][[j]][[3]]))
                    F[[i]][[3]][[j]][[3]][[k]][[3]] <- genF(F[[i]][[3]][[j]][[3]][[k]][[1]][1,],
                                                            F[[i]][[3]][[j]][[3]][[k]][[1]][2,])
    }

    ## F6
    if(generation > 5){
        for(i in 1:length(F))
            for(j in 1:length(F[[i]][[3]]))
                for(k in 1:length(F[[i]][[3]][[j]][[3]]))
                    for(l in 1:length(F[[i]][[3]][[j]][[3]][[k]][[3]]))
                        F[[i]][[3]][[j]][[3]][[k]][[3]][[l]][[3]] <- genF(F[[i]][[3]][[j]][[3]][[k]][[3]][[l]][[1]][1,],
                                                                          F[[i]][[3]][[j]][[3]][[k]][[3]][[l]][[1]][2,])
    }

    ## F7
    if(generation > 6){
        for(i in 1:length(F))
            for(j in 1:length(F[[i]][[3]]))
                for(k in 1:length(F[[i]][[3]][[j]][[3]]))
                    for(l in 1:length(F[[i]][[3]][[j]][[3]][[k]][[3]]))
                        for(m in 1:length(F[[i]][[3]][[j]][[3]][[k]][[3]][[l]][[3]]))
                            F[[i]][[3]][[j]][[3]][[k]][[3]][[l]][[3]][[m]][[3]] <-
                                genF(F[[i]][[3]][[j]][[3]][[k]][[3]][[l]][[3]][[m]][[1]][1,],
                                     F[[i]][[3]][[j]][[3]][[k]][[3]][[l]][[3]][[m]][[1]][2,])
    }

    return(F)
}