A probability tree allows to compute probabilities of complex events, such as genotype probabilities in intermediate generations of inbreeding through recurrent self-fertilization (selfing). This package implements functionality to compute probability trees for two- and three-marker genotypes in the F2 to F7 selfing generations. The conditional probabilities are derived automatically and in symbolic form. The package also provides functionality to extract and evaluate the relevant probabilities.
Copyright (c) 2014, Pioneer Hi-Bred International, Inc.
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buildSelfingTree generates the probability trees for
two- and three-marker genotypes. This is done by recursively calling
genSubtree.2M (two-marker genotypes) or
genSubtree.3M (three-marker genotypes). The core functionality of
deriving the symbolic conditional haplotype probabilities is implemented
haploProb.3M. The function
nodeProbabilities is used to symbolically multiply the
conditional probabilities along all branches and uses function
extractProbs to extract the conditional probabilities from the
trees. Finally function
evalProb symbolically sums the marginal
probabilities of relevant nodes and evaluates them with user specified
values for the recombination frequencies. The function
can be used to identify relevant events given a target genotype.
at Pioneer Hi-Bred International, Inc., Breeding Technologies, Johnson/IA, USA.
Maintainer: Frank Technow Frank.Technow@pioneer.com
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