Package: pedigreeTools 0.2
Paulino Perez Rodriguez
pedigreeTools: Versatile Functions for Working with Pedigrees
Tools to sort, edit and prune pedigrees and to extract the inbreeding coefficients and the relationship matrix (includes code for pedigrees from self-pollinated species). The use of pedigree data is central to genetics research within the animal and plant breeding communities to predict breeding values. The relationship matrix between the individuals can be derived from pedigree structure ('Vazquez et al., 2010') <doi:10.2527/jas.2009-1952>.
Authors:
pedigreeTools_0.2.tar.gz
pedigreeTools_0.2.zip(r-4.5)pedigreeTools_0.2.zip(r-4.4)pedigreeTools_0.2.zip(r-4.3)
pedigreeTools_0.2.tgz(r-4.4-x86_64)pedigreeTools_0.2.tgz(r-4.4-arm64)pedigreeTools_0.2.tgz(r-4.3-x86_64)pedigreeTools_0.2.tgz(r-4.3-arm64)
pedigreeTools_0.2.tar.gz(r-4.5-noble)pedigreeTools_0.2.tar.gz(r-4.4-noble)
pedigreeTools_0.2.tgz(r-4.4-emscripten)pedigreeTools_0.2.tgz(r-4.3-emscripten)
pedigreeTools.pdf |pedigreeTools.html✨
pedigreeTools/json (API)
| # Install 'pedigreeTools' in R: |
| install.packages('pedigreeTools', repos = c('https://rpedigree.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rpedigree/pedigreetools/issues
Last updated 11 months agofrom:a1c07cc8b8. Checks:OK: 7 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 05 2024 |
| R-4.5-win-x86_64 | NOTE | Sep 05 2024 |
| R-4.5-linux-x86_64 | NOTE | Sep 05 2024 |
| R-4.4-win-x86_64 | OK | Sep 05 2024 |
| R-4.4-mac-x86_64 | OK | Sep 05 2024 |
| R-4.4-mac-aarch64 | OK | Sep 05 2024 |
| R-4.3-win-x86_64 | OK | Sep 05 2024 |
| R-4.3-mac-x86_64 | OK | Sep 05 2024 |
| R-4.3-mac-aarch64 | OK | Sep 05 2024 |
Exports:DmateditPedgetAgetAInvgetASelfinggetASubsetgetDgetDInvgetGenAncestorsgetLgetLInvgetTgetTInvinbreedingped2DFpedigreeprunePedrelfactorrelfactorInv
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Mendelian sampling variance | Dmat getD getDInv |
| Edits a disordered or incomplete pedigree | editPed |
| Additive relationship matrix | getA |
| Inverse of the additive relationship matrix | getAInv |
| Extends the pedigree according to number of selfing cycles and also optionally computes the Additive Relationship Matrix for that pedigree. | getASelfing |
| Subset of additive relationship matrix | getASubset |
| Counts number of generations of ancestors for one subject. Use recursion. | getGenAncestors |
| Gene flow from a pedigree | getT |
| Inverse gene flow from a pedigree | getTInv |
| Inbreeding coefficients from a pedigree | inbreeding |
| Convert a pedigree to a data frame | ped2DF |
| Constructor for pedigree objects | pedigree |
| Pedigree class | pedigree-class pedinbred-class |
| Subsets a pedigree for a specified vector of individuals up to a specified number of previous generations using recursion. | prunePed |
| Relationship factor from a pedigree | getL relfactor |
| Inverse relationship factor from a pedigree | getLInv relfactorInv |