selfingTree: Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing

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.

Author
Frank Technow [aut, cre] (Pioneer Hi-Bred International, Inc., Johnston, Iowa)
Date of publication
2014-12-18 17:31:18
Maintainer
Frank Technow <Frank.Technow@pioneer.com>
License
BSD_3_clause + file LICENSE
Version
0.2

View on CRAN

Man pages

buildSelfingTree
Builds the probability tree
evalProb
Evaluates the genotype probability
extractProbs
Extracts conditional genotype probabilities
F4
Genotypes of one million simulated F4 lines.
genSubtree
Generates a sub-tree
getTargets
Obtain all possible genotypes that match a certain target...
haploProb
Probability of observing the target haplotype given the...
map
Genetic map of the three markers in the F4 data set.
nodeProbabilities
Multiplies conditional probabilities along all branches of...
selfingTree-package
Genotype Probabilities in Intermediate Generations of...

Files in this package

selfingTree
selfingTree/NAMESPACE
selfingTree/data
selfingTree/data/map.RData
selfingTree/data/datalist
selfingTree/data/F4.RData
selfingTree/R
selfingTree/R/evalProb.R
selfingTree/R/genSubtree.R
selfingTree/R/getTargets.R
selfingTree/R/nodeProbabilities.R
selfingTree/R/haploProb.R
selfingTree/R/buildSelfingTree.R
selfingTree/R/extractProbs.R
selfingTree/MD5
selfingTree/DESCRIPTION
selfingTree/man
selfingTree/man/getTargets.Rd
selfingTree/man/evalProb.Rd
selfingTree/man/map.Rd
selfingTree/man/selfingTree-package.Rd
selfingTree/man/nodeProbabilities.Rd
selfingTree/man/haploProb.Rd
selfingTree/man/genSubtree.Rd
selfingTree/man/F4.Rd
selfingTree/man/extractProbs.Rd
selfingTree/man/buildSelfingTree.Rd
selfingTree/LICENSE