selfingTree (version 0.2)

haploProb: Probability of observing the target haplotype given the parental genotype.

Description

These functions derive the symbolic formula for the probability of observing the target haplotype given the parental genotype.

Usage

haploProb.2M(gam1,gam2,target) ## two-marker genotypes
haploProb.3M(gam1,gam2,target) ## three-marker genotypes

Arguments

gam1,gam2

Three (three-marker genotypes) or two (two-marker genotypes) character string with the configuration of gamete one and two of the parental genotype.

target

Three (three-marker genotypes) or two (two-marker genotypes) character string with the configuration of the target haplotype.

Value

• A character string with the symbolic formula. For three-marker genotypes, x is the recombination frequency between markers 1 and 2 and y that between markers 2 and 3. For two-marker genotypes, z is the recombination frequency between markers 1 and 2.

Details

The idea behind the algorithm is to conceptually "recode" the alleles of the parental genotype into "target" and "non-target", where "target" is relative to the target haplotype. Then the rules are determined that would rearrange the gametes of the parental genotype into a "target-target-target" haplotype. These rearrangement rules are then translated into the symbolic formula.

Examples

haploProb.2M("AA","BB","AB")
haploProb.3M("AAA","BBB","ABA")