Package: statgenIBD 1.0.8
Bart-Jan van Rossum
statgenIBD: Calculation of IBD Probabilities
For biparental, three and four-way crosses Identity by Descent (IBD) probabilities can be calculated using Hidden Markov Models and inheritance vectors following Lander and Green (<https://www.jstor.org/stable/29713>) and Huang (<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Authors:
statgenIBD_1.0.8.tar.gz
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statgenIBD.pdf |statgenIBD.html✨
statgenIBD/json (API)
NEWS
| # Install 'statgenIBD' in R: |
| install.packages('statgenIBD', repos = c('https://biometris.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biometris/statgenibd/issues
Last updated 2 months agofrom:390598a715. Checks:1 OK, 11 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 07 2025 |
| R-4.5-win-x86_64 | NOTE | Mar 07 2025 |
| R-4.5-mac-x86_64 | NOTE | Mar 07 2025 |
| R-4.5-mac-aarch64 | NOTE | Mar 07 2025 |
| R-4.5-linux-x86_64 | NOTE | Mar 07 2025 |
| R-4.4-win-x86_64 | NOTE | Mar 07 2025 |
| R-4.4-mac-x86_64 | NOTE | Mar 07 2025 |
| R-4.4-mac-aarch64 | NOTE | Mar 07 2025 |
| R-4.4-linux-x86_64 | NOTE | Mar 07 2025 |
| R-4.3-win-x86_64 | NOTE | Mar 07 2025 |
| R-4.3-mac-x86_64 | NOTE | Mar 07 2025 |
| R-4.3-mac-aarch64 | NOTE | Mar 07 2025 |
Exports:calcIBDgetProbsreadIBDsreadRABBITwriteFlapjackwriteIBDs
Dependencies:clicolorspacecrayondata.tablefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressrlangscalessommerstatgenGWASstringitibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Concatenate function for objects of class IBDprob | c.IBDprob |
| Calculate IBD probabilities | calcIBD |
| Extract Probabilities for markers | getProbs |
| Plot function for objects of class IBDprob | plot.IBDprob |
| Read IBD probabilities from file | readIBDs |
| Read IBD probabilities | readRABBIT |
| Summary function for objects of class IBDprob | summary.IBDprob |
| Write to Flapjack format | writeFlapjack |
| Write IBD probabilities to file. | writeIBDs |
