# Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing

### Description

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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### Details

Package: | selfingTree |

Type: | Package |

Version: | 0.2 |

Date: | 2014-12-18 |

LazyData: | yes |

Depends: | foreach |

Function `buildSelfingTree`

generates the probability trees for
two- and three-marker genotypes. This is done by recursively calling
functions `genSubtree.2M`

(two-marker genotypes) or
`genSubtree.3M`

(three-marker genotypes). The core functionality of
deriving the symbolic conditional haplotype probabilities is implemented
in functions `haploProb.2M`

and `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 `getTargets`

can be used to identify relevant events given a target genotype.

### Author(s)

Frank Technow

at Pioneer Hi-Bred International, Inc., Breeding Technologies, Johnson/IA, USA.

Maintainer: Frank Technow Frank.Technow@pioneer.com