GRridge

DOI: 10.18129/B9.bioc.GRridge    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

PDF	R Script	GRridge
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Classification, GO, GeneExpression, GenePrediction, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, KEGG, Pathways, RNASeq, Regression, Software, Survival
Version	1.16.0
In Bioconductor since	BioC 3.5 (R-3.4) (4.5 years)
License	GPL-3
Depends	R (>= 3.2), penalized, Iso, survival, methods, graph, stats, glmnet, mvtnorm
Imports
LinkingTo
Suggests	testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GRridge_1.16.0.tar.gz
Windows Binary	GRridge_1.16.0.zip
macOS 10.13 (High Sierra)	GRridge_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GRridge
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GRridge
Package Short Url	https://bioconductor.org/packages/GRridge/
Package Downloads Report	Download Stats