Package: selfingTree 0.2
Frank Technow
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.
Authors:
selfingTree_0.2.tar.gz
selfingTree_0.2.tar.gz(r-4.5-noble)selfingTree_0.2.tar.gz(r-4.4-noble)
selfingTree_0.2.tgz(r-4.4-emscripten)selfingTree_0.2.tgz(r-4.3-emscripten)
selfingTree.pdf |selfingTree.html✨
selfingTree/json (API)
| # Install 'selfingTree' in R: |
| install.packages('selfingTree', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 10 years agofrom:6c6ce286ce. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-linux | OK | Aug 24 2024 |
Exports:buildSelfingTreeevalProbextractProbsgenSubtree.2MgenSubtree.3MgetTargetshaploProb.2MhaploProb.3MnodeProbabilities
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Genotype Probabilities in Intermediate Generations of Inbreeding Through Selfing | selfingTree-package selfingTree |
| Builds the probability tree | buildSelfingTree |
| Evaluates the genotype probability | evalProb |
| Extracts conditional genotype probabilities | extractProbs |
| Genotypes of one million simulated F4 lines. | F4 |
| Generates a sub-tree | genSubtree.2M genSubtree.3M |
| Obtain all possible genotypes that match a certain target configuration | getTargets |
| Probability of observing the target haplotype given the parental genotype. | haploProb.2M haploProb.3M |
| Genetic map of the three markers in the F4 data set. | map |
| Multiplies conditional probabilities along all branches of the tree | nodeProbabilities |