Genomic Regression Workbench

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


GROAN provides a workbench to compare the performances of different genomic regression models. GROAN also allows to study the effect of different kinds of noise on the regression accuracies. You have to input your data (phenotypes, genotypes/covariances, other covariates...), select your regressor(s) and optionally your noise injector. GROAN is crossvalidation-oriented (but masks all the related gritty details). Output is produced in numeric form and, if package ggplot2 is installed, as plots. Two small working datasets (GROAN.KI and GROAN.AI) are included and documented.

Installation

GROAN is installed as a standard R package. It leverages several other packages to implement genomic regressions. These packages are not installed by default, but set as suggested. GROAN will ask you to install any missing package as soon as you try to use it.

Dependencies

GROAN imports: plyr, rmarkdown, rrBLUP GROAN suggests: BGLR, e1071, ggplot2, knitr, randomForest

Documentation

Please see the package vignette for a complete tutorial. What follow is a minimal working example to give the gist of the tool.

nds = createNoisyDataset(
  name = 'PEA, normal noise',
  genotypes = GROAN.KI$SNPs,
  phenotypes = GROAN.KI$yield,
  noiseInjector = noiseInjector.norm,
  mean = 0,
  sd = sd(GROAN.KI$yield) * 0.5
)
 
#2) creating a GROAN.WorkBench using default regressor and crossvalidation preset
wb = createWorkbench()
 
#3) running the experiment
res = GROAN.run(nds, wb)
 
#4) examining results
summary(res)
plotResult(res)

News

Changes in 1.1:

  • GROAN.run now supports test on datasets different from the one used for training. Its interface, GROAN.Result object and plotResult function were changed accordingly
  • a second pea dataset, GROAN.AI, was included, and the old dataset was refactored as GROAN.KI
  • old dataset notation (GROAN.pea.SNPs, GROAN.pea.yield, GROAN.pea.kinship) was maintained but marked as deprecated in documentation
  • added or improved print and summary function for all GROAN objects

Reference manual

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install.packages("GROAN")

1.2.0 by Nelson Nazzicari, 9 days ago


Browse source code at https://github.com/cran/GROAN


Authors: Nelson Nazzicari & Filippo Biscarini


Documentation:   PDF Manual  


GPL-3 | file LICENSE license


Imports plyr, rrBLUP

Suggests BGLR, e1071, ggplot2, knitr, randomForest


See at CRAN