The statgenMPP package | Example simulated data | Example maize | Example barley | Parallel computing | Summary | References
Package: statgenMPP 1.0.5
Bart-Jan van Rossum
statgenMPP: QTL Mapping for Multi Parent Populations
For Multi Parent Populations (MPP) Identity By Descend (IBD) probabilities are computed using Hidden Markov Models. These probabilities are then used in a mixed model approach for QTL Mapping as described in Li et al. (<doi:10.1007/s00122-021-03919-7>).
Authors:
statgenMPP_1.0.5.tar.gz
statgenMPP_1.0.5.zip(r-4.7)statgenMPP_1.0.5.zip(r-4.6)statgenMPP_1.0.5.zip(r-4.5)
statgenMPP_1.0.5.tgz(r-4.6-any)statgenMPP_1.0.5.tgz(r-4.5-any)
statgenMPP_1.0.5.tar.gz(r-4.7-any)statgenMPP_1.0.5.tar.gz(r-4.6-any)
statgenMPP_1.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
statgenMPP/json (API)
| # Install 'statgenMPP' in R: |
| install.packages('statgenMPP', repos = c('https://biometris.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biometris/statgenmpp/issues
Datasets:
- barleyMQM - Pre-computed MQM output barley
- barleyPheno - Phenotypic data for awn length in barley
- maizeMQM - Pre-computed MQM output maize
- maizeSQM - Pre-computed SQM output maize
Last updated from:b1178c8a93. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 159 | ||
| source / vignettes | OK | 207 | ||
| linux-release-x86_64 | OK | 199 | ||
| macos-release-arm64 | OK | 102 | ||
| macos-oldrel-arm64 | OK | 123 | ||
| windows-devel | OK | 111 | ||
| windows-release | OK | 116 | ||
| windows-oldrel | OK | 117 | ||
| wasm-release | OK | 114 |
Exports:calcIBDMPPcreateGDataMPPkinshipIBDreadRABBITMPPselQTLMPP
Dependencies:clicodetoolscpp11crayondata.tabledotCall64enhancerfarverforeachggplot2gluegridExtragtableisobanditeratorslabelinglatticelifecycleLMMsolverMASSMatrixR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloRcppProgressrlangS7scalessommerspamstatgenGWASstatgenIBDstringivctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Pre-computed MQM output barley | barleyMQM |
| Phenotypic data for awn length in barley | barleyPheno |
| IBD calculation for multi parental populations | calcIBDMPP |
| Create an object of class gDataMPP | createGDataMPP |
| Compute kinship matrix for IBD probabilities | kinshipIBD |
| Pre-computed MQM output maize | maizeMQM |
| Pre-computed SQM output maize | maizeSQM |
| Plot function for the class 'gDataMPP' | plot.gDataMPP |
| Plot function for the class 'QTLMPP' | plot.QTLMPP |
| Print summary of object of class 'summary.QTLMPP' | print.summary.QTLMPP |
| Read IBD probabilities | readRABBITMPP |
| Multi round genome scans for QTL detection | selQTLMPP |
| Summary function for the class 'gDataMPP' | summary.gDataMPP |
| Summary function for the class 'QTLMPP' | summary.QTLMPP |
