selfingTree (version 0.2)

extractProbs: Extracts conditional genotype probabilities

Description

This function extracts the symbolic formulas for the conditional genotype probabilities from the uppermost level of the (sub)tree.

Usage

extractProbs(F)

Arguments

F

A sub-tree in the format generated by function genSubtree.2M or genSubtree.3M.

Value

• A character vector with the symbolic formulas. For three-marker genotypes, symbol x is the recombination frequency between markers 1 and 2 and y that between markers 2 and 3. For two-marker genotypes, symbol z is the recombination frequency between markers 1 and 2. The names of the elements indicate the allelic configuration of the two gametes comprising the genotype as gamete1-gamete2 (e.g., "AAB-AAA"). The elements sum to 1.

Examples

probs.2M <- extractProbs(genSubtree.2M("BA","AA"))
probs.3M <- extractProbs(genSubtree.3M("BAA","AAB"))

## must sum to 1
stopifnot(all.equal(evalProb(probs.2M, z = 0.044),1))
stopifnot(all.equal(evalProb(probs.3M, x = 0.123, y = 0.344),1))