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:Luke Jostins

Mangrove_1.21.tar.gz
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Mangrove_1.21.tgz(r-4.4-any)Mangrove_1.21.tgz(r-4.3-any)
Mangrove_1.21.tar.gz(r-4.5-noble)Mangrove_1.21.tar.gz(r-4.4-noble)
Mangrove_1.21.tgz(r-4.4-emscripten)Mangrove_1.21.tgz(r-4.3-emscripten)
Mangrove.pdf |Mangrove.html✨
Mangrove/json (API)
NEWS

# 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

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.65 score 15 scripts 468 downloads 3 mentions 33 exports 0 dependencies

Last updated 8 years agofrom:a302411add. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 20 2024
R-4.5-win	NOTE	Nov 20 2024
R-4.5-linux	NOTE	Nov 20 2024
R-4.4-win	NOTE	Nov 20 2024
R-4.4-mac	NOTE	Nov 20 2024
R-4.3-win	OK	Nov 20 2024
R-4.3-mac	OK	Nov 20 2024

Exports:applyBetas applyORs calcBetas calcORs getVarExp getVarExpSim initialiseTree plot.MangroveBetas plot.MangroveContPreds plot.MangroveORs plot.MangrovePed plot.MangroveRiskPreds plot.MangroveSample plot.MangroveTree plotNaivePrev plotSampledPrev print.MangroveBetas print.MangroveContPreds print.MangroveORs print.MangrovePed print.MangroveRiskPreds print.MangroveSample print.MangroveTree readBetas readORs readPed summary.MangroveBetas summary.MangroveContPreds summary.MangroveORs summary.MangrovePed summary.MangroveRiskPreds summary.MangroveSample summary.MangroveTree

Dependencies:

Mangrove

Rendered fromMangrove.Rnwusingutils::Sweaveon Nov 20 2024.

Last update: 2017-02-22
Started: 2017-02-22

Citation

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