GRridge

This package is for version 3.16 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: 3.16

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 "4.2") 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 1.22.0
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
URL
See More
Suggests testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GRridge_1.22.0.tar.gz
Windows Binary GRridge_1.22.0.zip (64-bit only)
macOS Binary (x86_64) GRridge_1.21.0.tgz
macOS Binary (arm64) GRridge_1.22.0.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 3.16 Source Archive