haploProb {selfingTree} | R Documentation |
These functions derive the symbolic formula for the probability of observing the target haplotype given the parental genotype.
haploProb.2M(gam1,gam2,target) ## two-marker genotypes
haploProb.3M(gam1,gam2,target) ## three-marker genotypes
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. |
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.
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.
Frank Technow
haploProb.2M("AA","BB","AB")
haploProb.3M("AAA","BBB","ABA")