selfingTree: Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing
Version 0.2

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.

AuthorFrank Technow [aut, cre] (Pioneer Hi-Bred International, Inc., Johnston, Iowa)
Date of publication2014-12-18 17:31:18
MaintainerFrank Technow <Frank.Technow@pioneer.com>
LicenseBSD_3_clause + file LICENSE
Version0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("selfingTree")

Getting started

Package overview

Popular man pages

buildSelfingTree: Builds the probability tree
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...
nodeProbabilities: Multiplies conditional probabilities along all branches of...
selfingTree-package: Genotype Probabilities in Intermediate Generations of...
See all...

All man pages Function index File listing

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...

Functions

F4 Man page
buildSelfingTree Man page Source code
evalProb Man page Source code
extractProbs Man page Source code
genSubtree.2M Man page Source code
genSubtree.3M Man page Source code
getTargets Man page Source code
haploProb.2M Man page Source code
haploProb.3M Man page Source code
map Man page
nodeProbabilities Man page Source code
selfingTree Man page
selfingTree-package Man page

Files

NAMESPACE
data
data/map.RData
data/datalist
data/F4.RData
R
R/evalProb.R
R/genSubtree.R
R/getTargets.R
R/nodeProbabilities.R
R/haploProb.R
R/buildSelfingTree.R
R/extractProbs.R
MD5
DESCRIPTION
man
man/getTargets.Rd
man/evalProb.Rd
man/map.Rd
man/selfingTree-package.Rd
man/nodeProbabilities.Rd
man/haploProb.Rd
man/genSubtree.Rd
man/F4.Rd
man/extractProbs.Rd
man/buildSelfingTree.Rd
LICENSE
selfingTree documentation built on May 19, 2017, 8:34 p.m.

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