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("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 | R Script | |
| Reference Manual | ||
| 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 | |
| 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_1.8.0.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 |