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selfingTree (version 0.2)

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.

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Version

Install

install.packages('selfingTree')

Monthly Downloads

160

Version

0.2

License

BSD_3_clause + file LICENSE

Maintainer

Frank Technow

Last Published

December 18th, 2014

Functions in selfingTree (0.2)

selfingTree-package

Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing
buildSelfingTree

Builds the probability tree
F4

Genotypes of one million simulated F4 lines.
getTargets

Obtain all possible genotypes that match a certain target configuration
map

Genetic map of the three markers in the F4 data set.
genSubtree

Generates a sub-tree
evalProb

Evaluates the genotype probability
nodeProbabilities

Multiplies conditional probabilities along all branches of the tree
haploProb

Probability of observing the target haplotype given the parental genotype.
extractProbs

Extracts conditional genotype probabilities