Package: pedprobr 0.9.4
Magnus Dehli Vigeland
pedprobr: Probability Computations on Pedigrees
An implementation of the Elston-Stewart algorithm for calculating pedigree likelihoods given genetic marker data (Elston and Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is extended to allow inbred founders. 'pedprobr' is part of the 'ped suite', a collection of packages for pedigree analysis in R. In particular, 'pedprobr' depends on 'pedtools' for pedigree manipulations and 'pedmut' for mutation modelling. For more information, see 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
Authors:
pedprobr_0.9.4.tar.gz
pedprobr_0.9.4.zip(r-4.5)pedprobr_0.9.4.zip(r-4.4)pedprobr_0.9.4.zip(r-4.3)
pedprobr_0.9.4.tgz(r-4.4-any)pedprobr_0.9.4.tgz(r-4.3-any)
pedprobr_0.9.4.tar.gz(r-4.5-noble)pedprobr_0.9.4.tar.gz(r-4.4-noble)
pedprobr_0.9.4.tgz(r-4.4-emscripten)pedprobr_0.9.4.tgz(r-4.3-emscripten)
pedprobr.pdf |pedprobr.html✨
pedprobr/json (API)
NEWS
| # Install 'pedprobr' in R: |
| install.packages('pedprobr', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/magnusdv/pedprobr/issues
Last updated 7 months agofrom:4734c2d5d5. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 04 2024 |
| R-4.5-win | NOTE | Nov 04 2024 |
| R-4.5-linux | NOTE | Nov 04 2024 |
| R-4.4-win | OK | Nov 04 2024 |
| R-4.4-mac | OK | Nov 04 2024 |
| R-4.3-win | OK | Nov 04 2024 |
| R-4.3-mac | OK | Nov 04 2024 |
Exports:allGenotypescheckMerlingenoCombinationshaldaneHWprobkosambilikelihoodlikelihood2likelihoodMerlinlumpAllelesmerlinoneMarkerDistributionsetMutationModeltwoMarkerDistribution
Dependencies:evaluatehighrkinship2knitrlatticeMatrixpedmutpedtoolsquadprogxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Genotype matrix | allGenotypes |
| Genotype combinations | genoCombinations |
| Genetic map functions | haldane kosambi |
| Hardy-Weinberg probabilities | HWprob |
| Pedigree likelihood | likelihood likelihood.list likelihood.ped likelihood2 likelihood2.list likelihood2.ped |
| Allele lumping | lumpAlleles |
| Pedigree likelihoods computed by MERLIN | checkMerlin likelihoodMerlin merlin |
| Genotype distribution for a single marker | oneMarkerDistribution |
| Set a mutation model | setMutationModel |
| Genotype distribution for two linked markers | twoMarkerDistribution |