clusterAlgorithmClara-class {goCluster} | R Documentation

## Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets

### Description

This can be used to group a dataset according to partitioning around medoids. The resulting gene groups can subsequently be analysed for significant enrichment of specific annotations.

### Details

The class provides a wrapper around the `clusterclara` function. Please read the corresponding documentation for further details.

### Slots

`clusters`:
  Object of class `"numeric"`, determines the number of clusters the partitioning around medoids will identify.
`repeats`:
  Object of class `"numeric"`, specifies how often the clustering is repeated in case clara is not run with a fixed initialization.
`fixed`:
  Object of class `"logical"`, if true, a fixed seed will be used for the partitioning around medoids.
`distance`:
  Object of class `"character"`, specifies the distance matrix that will be used.

Additional slots are described in the documentation of the `clusterAlgorithm-class` and `clusterModule-class`.

### Extends

Class `"clusterAlgorithm"`, directly. Class `"clusterModule"`, by class `"clusterAlgorithm"`.

### Methods

config
  `signature(object = "clusterAlgorithmClara")`: interactive setup of the class. You will be asked to specify the number of clusters clara clustering should result in and whether a fixed seed should be used. If not the class offers to repeat the clustering. In addition the distance matrix needs to be defined.
setup
  `signature(object = "clusterAlgorithmClara")`: returns the configuration of the object as a list. This list can again be used for the non-interactive setup of the class.
setup<-
  `signature(object = "clusterAlgorithmClara")`: non-interactive setup of the class. The options are specified using a list.
execute
  `signature(object = "clusterAlgorithmClara")`: run the clustering.
reset
  `signature(object = "clusterAlgorithmClara")`: remove all cluster data so that the `execute` function can be run again.
print
  `signature(object = "clusterAlgorithmClara")`: This function prints some basic information about the content of this object.

### Author(s)

Gunnar Wrobel, work@gunnarwrobel.de, http://www.gunnarwrobel.de.

### See Also

`clusterclara`, `goCluster-class`, `clusterModule-class`, `clusterAlgorithm-class`, `clusterAlgorithmKmeans-class`, `clusterAlgorithmPam-class`, `clusterAlgorithmHclust-class`, .

### Examples

    ## Predefined setup for goCluster
    ## (This configuration selects the
    ## clara clustering)
    data(benomylsetup)

    ## Setup a new goCluster object
    test <- new("goCluster")
    setup(test) <- benomylsetup

    ## Retrieve annotation
    test@data <- execute(test@data, test)

    ## Cluster the dataset
    test@algo <- execute(test@algo, test)

[Package goCluster version 1.4.0 Index]