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.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

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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