Package: statgenIBD 1.0.11

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:Martin Boer [aut], Bart-Jan van Rossum [aut, cre], Wenhao Li [ctb], Johannes Kruisselbrink [ctb]

statgenIBD_1.0.11.tar.gz
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statgenIBD_1.0.11.tgz(r-4.6-x86_64)statgenIBD_1.0.11.tgz(r-4.6-arm64)statgenIBD_1.0.11.tgz(r-4.5-x86_64)statgenIBD_1.0.11.tgz(r-4.5-arm64)
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statgenIBD_1.0.11.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
statgenIBD/json (API)

# 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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

geneticshmmibdcpp

5.52 score 1 packages 11 scripts 337 downloads 6 exports 35 dependencies

Last updated from:4703dcf8c3. Checks:11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE215
linux-devel-x86_64NOTE225
source / vignettesOK284
linux-release-arm64NOTE222
linux-release-x86_64NOTE221
macos-release-arm64NOTE204
macos-release-x86_64NOTE287
macos-oldrel-arm64NOTE122
macos-oldrel-x86_64NOTE298
windows-develNOTE161
windows-releaseNOTE174
windows-oldrelNOTE152
wasm-releaseOK259

Exports:calcIBDgetProbsreadIBDsreadRABBITwriteFlapjackwriteIBDs

Dependencies:clicpp11crayondata.tabledotCall64enhancerfarverggplot2gluegtableisobandlabelinglatticelifecycleLMMsolverMASSMatrixR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloRcppProgressrlangS7scalessommerspamstatgenGWASstringivctrsviridisLitewithr

IBD calculations using statgenIBD
The statgenIBD package | Population types | Examples | Steptoe Morex | Visualizing results | Pedigree plot | Genetic map plot | Single genotype plot | Plot of IBD probabilities for all genotypes. | Plot the coverage of each parent across the genome. | Plot the total coverage of each parent | Evaluation positions | Extracting value for markers of interest | Write and read tab-delimited *.txt files | Write results to Flapjack format | Simulated data | F4 | C4S3 | Multi-cross | Importing IBD probabilities computed using RABBIT | References
Rendered fromIBDCalculations.Rmdusingknitr::rmarkdown

Last update: 2025-07-01
Started: 2021-06-25

IBD probabilities file format
File format | Examples | Writing IBD probabilities to a file | Reading IBD probabilities from file
Rendered fromIBDFileFormat.Rmdusingknitr::rmarkdown

Last update: 2022-08-24
Started: 2022-08-08