R/genSubtree.R

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

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

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genSubtree.2M <- function(gam1,gam2){

    
    F <- list()

    ## generate all possible gametes from parent genotype
    L1 <- paste(substr(gam1,1,1),substr(gam2,1,1),sep="")
    L2 <- paste(substr(gam1,2,2),substr(gam2,2,2),sep="")

    AB.series <- unique(paste(rep(c(substr(L1,1,1),substr(L1,2,2)),each = 2),
                              rep(c(substr(L2,1,1),substr(L2,2,2)),2),
                              sep = ""))

    for(AB1 in AB.series){
        for(AB2 in AB.series){

            geno.prob <- paste(haploProb.2M(gam1,gam2,AB1),
                               haploProb.2M(gam1,gam2,AB2),
                               sep = "*")

            F[[length(F) + 1]] <- list(rbind(AB1,AB2),geno.prob)
       
        }
    }

    return(F)    
}



genSubtree.3M <- function(gam1,gam2){
    
    F <- list()

    L1 <- paste(substr(gam1,1,1),substr(gam2,1,1),sep="")
    L2 <- paste(substr(gam1,2,2),substr(gam2,2,2),sep="")
    L3 <- paste(substr(gam1,3,3),substr(gam2,3,3),sep="")


    AB.series <- unique(paste(rep(c(substr(L1,1,1),substr(L1,2,2)),each = 4),
                              rep(rep(c(substr(L2,1,1),substr(L2,2,2)),each = 2),2),
                              rep(c(substr(L3,1,1),substr(L3,2,2)), 4),
                              sep = ""))

    for(AB1 in AB.series){
        for(AB2 in AB.series){

            geno.prob <- paste(haploProb.3M(gam1,gam2,AB1),
                               haploProb.3M(gam1,gam2,AB2),
                               sep = "*")

            F[[length(F) + 1]] <- list(rbind(AB1,AB2),geno.prob)
       
        }
    }

    return(F)
    
}