Package: GROAN 1.3.1

GROAN: Genomic Regression Workbench

Workbench for testing genomic regression accuracy on (optionally noisy) phenotypes.

Authors:Nelson Nazzicari & Filippo Biscarini

# Install 'GROAN' in R:

install.packages('GROAN', repos = c('https://ne1s0n.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

On CRAN:

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

Last updated from:5a84045a9a. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	115
source / vignettes	OK	171
linux-release-x86_64	OK	113
macos-release-arm64	OK	170
macos-oldrel-arm64	OK	136
windows-devel	OK	81
windows-release	OK	90
windows-oldrel	OK	80
wasm-release	OK	213

Dependencies:plyr Rcpp rrBLUP

Last update: 2022-11-28
Started: 2017-07-12

Help page	Topics
Add an extra regressor to a Workbench	addRegressor
Check two GROAN.NoisyDataSet for dimension compatibility	are.compatible
Noisy Data Set Constructor	createNoisyDataset
Generate a random run id	createRunId
Workbench constructor	createWorkbench
Generate an instance of noisy phenotypes	getNoisyPhenotype
Example data for pea AI lines	GROAN.AI
Example data for pea KI lines	GROAN.KI
[DEPRECATED]	GROAN.pea.kinship
[DEPRECATED]	GROAN.pea.SNPs
[DEPRECATED]	GROAN.pea.yield
Compare Genomic Regressors on a Noisy Dataset	GROAN.run
Measure Performance of a Prediction	measurePredictionPerformance
Function to calculate mean Normalized Discounted Cumulative Gain (NDCG)	ndcg
Noise Injector dummy function	noiseInjector.dummy
Inject Normal Noise	noiseInjector.norm
Swap phenotypes between samples	noiseInjector.swapper
Inject Uniform Noise	noiseInjector.unif
Regression using BGLR package	phenoRegressor.BGLR
Multi-matrix GBLUP using BGLR	phenoregressor.BGLR.multikinships
Regression dummy function	phenoRegressor.dummy
Random Forest Regression using package randomForest	phenoRegressor.RFR
SNP-BLUP or G-BLUP using rrBLUP package	phenoRegressor.rrBLUP
Support Vector Regression using package e1071	phenoRegressor.SVR
Plot results of a run	plotResult
Print a GROAN Noisy Dataset object	print.GROAN.NoisyDataset
Print a GROAN Workbench object	print.GROAN.Workbench
Summary for GROAN Noisy Dataset object	summary.GROAN.NoisyDataset
Summary of GROAN.Result	summary.GROAN.Result