selfingTree-package: 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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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.Details
ll{
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.