GRridge-package {GRridge} | R Documentation

## Implements adaptive group-regularized (logistic) ridge regression by use of co-data.

### Description

This package implements adaptive group-regularized (logistic) ridge regression by use of co-data. It uses co-data to improve predictions of binary and continuous response from high-dimension (e.g. genomics) data. Here, co-data is auxiliary information on variables (e.g. genes), such as annotation or p-values from other studies. The package includes convenience functions to convert such co-data to the correct input format. In additiion, in includes functions for evaluating the predictive performance.

### Details

Package: | GRridge
Type: | Package
Version: | 1.7.3
Date: | 2018-11-29
License: | GPL

Main functions in the GRridge package are:

`auc`: Computes Area-under-the-ROC-curve
`CreatePartition`: Creates a partition (groups) of variables
`dataFarkas`: Large data set plus external information
`dataSimlin`: Small simulated data set with linear response
`dataVerlaat`: Methylation data plus external information
`dataWurdinger`: RNAseq data plus external information
`simlinsmall`: Simulated data for linear regression
`grridge`: Group-regularized (logistic, survival) ridge regression
`grridgeCV`: Cross-validated predictions for a `grridge` (logistic, survival) regression.
`matchGeneSets`: Creates a grouping of variables (genes) from gene sets
`mergeGroups`: Merge groups in a partition
`PartitionsSelection`: Co-data selection in a Group-regularized ridge regression model
`predict.grridge`: Predictions for new samples from a `grridge` object
`roc`: Computes an ROC-curve for probabilistic classifiers

### Author(s)

Mark A. van de Wiel (mark.vdwiel@vumc.nl), Putri Novianti (p.novianti@vumc.nl)

### References

Mark van de Wiel, Tonje Lien, Wina Verlaat, Wessel van Wieringen, Saskia Wilting. (2016). Better prediction by use of co-data: adaptive group-regularized ridge regression. Statistics in Medicine, 35(3), 368-81.

Novianti PW, Snoek B, Wilting SM, van de Wiel MA (2017). Better diagnostic signatures from RNAseq data through use of auxiliary co-data. Bioinformatics, 33, 1572-1574.

### See Also

`GRridge` depends on: `penalized`. Examples: `grridge`

[Package GRridge version 1.10.0 Index]