GROAN1.3.1 package

Genomic Regression Workbench

addRegressor

Add an extra regressor to a Workbench

are.compatible

Check two GROAN.NoisyDataSet for dimension compatibility

artificialGenotypes

Create a set of artificial genotypes

artificialPhenotypes

Create a set of artificial phenotypes

createNoisyDataset

Noisy Data Set Constructor

createRunId

Generate a random run id

createWorkbench

Workbench constructor

dummy.function

Dummy function for import management

getExtraCovariatesNames

String of extra covariates names

getNoisyPhenotype

Generate an instance of noisy phenotypes

GROAN.run

Compare Genomic Regressors on a Noisy Dataset

is.boolean

Is a boolean?

is.in.range

Is in the passed numeric range

is.naturalnumber

Is a positive integer?

is.single.slot

Is a single slot thing?

is.string

Is a string?

measurePredictionPerformance

Measure Performance of a Prediction

ndcg

Function to calculate mean Normalized Discounted Cumulative Gain (NDCG...

noiseInjector.dummy

Noise Injector dummy function

noiseInjector.norm

Inject Normal Noise

noiseInjector.swapper

Swap phenotypes between samples

noiseInjector.unif

Inject Uniform Noise

phenoregressor.BGLR.multikinships

Multi-matrix GBLUP using BGLR

phenoRegressor.BGLR

Regression using BGLR package

phenoRegressor.dummy

Regression dummy function

phenoRegressor.RFR

Random Forest Regression using package randomForest

phenoRegressor.rrBLUP.G

G-BLUP using rrBLUP library

phenoRegressor.rrBLUP

SNP-BLUP or G-BLUP using rrBLUP package

phenoRegressor.rrBLUP.SNP

SNP-BLUP using rrBLUP library

phenoRegressor.SVR

Support Vector Regression using package e1071

plotResult

Plot results of a run

print.GROAN.NoisyDataset

Print a GROAN Noisy Dataset object

print.GROAN.Workbench

Print a GROAN Workbench object

stratified_crossvalidation_folds

Assignments for stratified crossvalidation

summary.GROAN.NoisyDataset

Summary for GROAN Noisy Dataset object

summary.GROAN.Result

Summary of GROAN.Result

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

  • Maintainer: Nelson Nazzicari
  • License: GPL-3 | file LICENSE
  • Last published: 2022-11-28