GRridge

DOI: 10.18129/B9.bioc.GRridge    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see GRridge.

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

Bioconductor version: 3.15

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")

 

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 1.20.0
In Bioconductor since BioC 3.5 (R-3.4) (5.5 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_1.20.0.tar.gz
Windows Binary
macOS Binary (x86_64) GRridge_1.20.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: