Simulate admixed population | Unsupervised global admixture inference | Semi-supervised global admixture inference | Local admixture inference | Import genotyping data
This package is considered a duplicate. The official version of this package is found at:https://simonrio.r-universe.dev/AdmixPoly
Package: AdmixPoly 1.0.1
Simon Rio
AdmixPoly: Global and Local Admixture Inference in Polyploids
Provides functions to perform global (genome-wide) and local admixture inference from bi- and multi-allelic marker dosages (discrete or continuous) in polyploid species.
Authors:
AdmixPoly_1.0.1.tar.gz
AdmixPoly_1.0.1.zip(r-4.7-x86_64)AdmixPoly_1.0.1.zip(r-4.7-arm64)AdmixPoly_1.0.1.zip(r-4.6-x86_64)AdmixPoly_1.0.1.zip(r-4.6-arm64)
AdmixPoly_1.0.1.tar.gz(r-4.7-arm64)AdmixPoly_1.0.1.tar.gz(r-4.7-x86_64)AdmixPoly_1.0.1.tar.gz(r-4.6-arm64)AdmixPoly_1.0.1.tar.gz(r-4.6-x86_64)
AdmixPoly_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
AdmixPoly/json (API)
| # Install 'AdmixPoly' in R: |
| install.packages('AdmixPoly', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Uses libs:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:9f516f8592. Checks:10 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 138 | ||
| linux-devel-x86_64 | OK | 237 | ||
| source / vignettes | OK | 261 | ||
| linux-release-arm64 | OK | 141 | ||
| linux-release-x86_64 | OK | 183 | ||
| windows-devel-arm64 | OK | 275 | ||
| windows-devel-x86_64 | OK | 219 | ||
| windows-release-arm64 | OK | 264 | ||
| windows-release-x86_64 | OK | 195 | ||
| wasm-release | OK | 129 |
Exports:AdmixGlobalAdmixLocalGlobalPlotLocalPlotReadHPAReadVCFSimulatePop
Dependencies:clicpp11data.tabledplyrfarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadillorlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| AdmixPoly: Global and Local Admixture Inference in Polyploids | AdmixPoly-package AdmixPoly |
| Expectation-Maximization algorithm for global (genome-wide) admixture inference | AdmixGlobal |
| Forward-Backward algorithm for local admixture inference | AdmixLocal |
| Calculate the log-likelihood | ComputeLogLik |
| Plot global admixture proportions | GlobalPlot |
| Plot local ancestry dosages | LocalPlot |
| Read Haplotype Presence-Absence (HPA) file | ReadHPA |
| Read VCF file | ReadVCF |
| Simulate an admixed polyploid population characterized for multi-allelic markers | SimulatePop |
| Update Prop and Freq parameters for EM step | UpdateParam |