extractProbs: Extracts conditional genotype probabilities

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

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.

Author(s)

Frank Technow

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))

selfingTree documentation built on May 2, 2019, 8:17 a.m.