GRridge

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GRridge.

Better prediction by use of co-data: Adaptive group-regularized ridge regression


Bioconductor version: 3.9

This package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.

Author: Mark A. van de Wiel <mark.vdwiel at vumc.nl>, Putri W. Novianti <p.novianti at vumc.nl>

Maintainer: Mark A. van de Wiel <mark.vdwiel at vumc.nl>

Citation (from within R, enter citation("GRridge")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GRridge")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GRridge")
GRridge PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, Classification, GO, GeneExpression, GenePrediction, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, KEGG, Pathways, RNASeq, Regression, Software, Survival
Version 1.8.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 3.2), penalized, Iso, survival, methods, graph, stats, glmnet, mvtnorm
Imports
System Requirements
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Suggests testthat
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GRridge_1.8.0.tar.gz
Windows Binary GRridge_1.8.0.zip
Mac OS X 10.11 (El Capitan) GRridge_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GRridge
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GRridge
Bioc Package Browser https://code.bioconductor.org/browse/GRridge/
Package Short Url https://bioconductor.org/packages/GRridge/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive