Package: Mangrove 1.21
Mangrove: Risk Prediction on Trees
Methods for performing genetic risk prediction from genotype data. You can use it to perform risk prediction for individuals, or for families with missing data.
Authors:
Mangrove_1.21.tar.gz
Mangrove_1.21.zip(r-4.7)Mangrove_1.21.zip(r-4.6)Mangrove_1.21.zip(r-4.5)
Mangrove_1.21.tgz(r-4.6-any)Mangrove_1.21.tgz(r-4.5-any)
Mangrove_1.21.tar.gz(r-4.7-any)Mangrove_1.21.tar.gz(r-4.6-any)
Mangrove_1.21.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Mangrove/json (API)
| # Install 'Mangrove' in R: |
| install.packages('Mangrove', repos = c('https://lowk.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- ccped - Example data for the Mangrove vignette
- contped - Example data for the Mangrove vignette
- exampleBetas - Example data for the Mangrove vignette
- exampleORs - Example data for the Mangrove vignette
- famped - Example data for the Mangrove vignette
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:a302411add. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 146 | ||
| source / vignettes | OK | 140 | ||
| linux-release-x86_64 | NOTE | 114 | ||
| macos-release-arm64 | NOTE | 137 | ||
| macos-oldrel-arm64 | NOTE | 170 | ||
| windows-devel | NOTE | 101 | ||
| windows-release | NOTE | 87 | ||
| windows-oldrel | NOTE | 62 | ||
| wasm-release | OK | 96 |
Exports:applyBetasapplyORscalcBetascalcORsgetVarExpgetVarExpSiminitialiseTreeplot.MangroveBetasplot.MangroveContPredsplot.MangroveORsplot.MangrovePedplot.MangroveRiskPredsplot.MangroveSampleplot.MangroveTreeplotNaivePrevplotSampledPrevprint.MangroveBetasprint.MangroveContPredsprint.MangroveORsprint.MangrovePedprint.MangroveRiskPredsprint.MangroveSampleprint.MangroveTreereadBetasreadORsreadPedsummary.MangroveBetassummary.MangroveContPredssummary.MangroveORssummary.MangrovePedsummary.MangroveRiskPredssummary.MangroveSamplesummary.MangroveTree
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Mangrove: Risk prediction on trees | Mangrove-package Mangrove |
| Calculating liability-scale variance explained by genetic risk variants | getVarExp getVarExpSim |
| The MangroveBetas class | MangroveBetas plot.MangroveBetas print.MangroveBetas readBetas summary.MangroveBetas |
| The MangroveContPreds class | applyBetas calcBetas MangroveContPreds plot.MangroveContPreds print.MangroveContPreds summary.MangroveContPreds |
| Example data for the Mangrove vignette | ccped contped exampleBetas exampleORs famped MangroveExamples |
| The MangroveORs class | MangroveORs plot.MangroveORs print.MangroveORs readORs summary.MangroveORs |
| The MangrovePed class | MangrovePed plot.MangrovePed print.MangrovePed readPed summary.MangrovePed |
| The MangroveRiskPreds class | applyORs calcORs MangroveRiskPreds plot.MangroveRiskPreds print.MangroveRiskPreds summary.MangroveRiskPreds |
| The MangroveSample class | MangroveSample plot.MangroveSample print.MangroveSample summary.MangroveSample |
| The MangroveTree class | addPed getPrevs initialiseTree MangroveTree plot.MangroveTree print.MangroveTree summary.MangroveTree |
| Plotting expected | plotNaivePrev plotSampledPrev |
