selfingTree-package {selfingTree}

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.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

Neither the name of Pioneer Hi-Bred International, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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 [e-mail]