BioConductor

GRridge 1.4.0

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

Released Apr 4, 2018 by Mark A. van de Wiel

This package can be loaded by Renjin but 3 out 14 tests failed.

Dependencies

glmnet 2.0-16 graph 1.58.0 survival 2.42-3 mvtnorm 1.0-8 penalized 0.9-50 Iso 0.0-17

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.

Installation

Maven

This package can be included as a dependency from a Java or Scala project by including the following your project's pom.xml file. Read more about embedding Renjin in JVM-based projects.

<dependencies>
  <dependency>
    <groupId>org.renjin.bioconductor</groupId>
    <artifactId>GRridge</artifactId>
    <version>1.4.0-b2</version>
  </dependency>
</dependencies>
<repositories>
  <repository>
    <id>bedatadriven</id>
    <name>bedatadriven public repo</name>
    <url>https://nexus.bedatadriven.com/content/groups/public/</url>
  </repository>
</repositories>

View build log

Renjin CLI

If you're using Renjin from the command line, you load this library by invoking:

library('org.renjin.bioconductor:GRridge')

Test Results

This package was last tested against Renjin 0.9.2644 on Jun 2, 2018.