goCluster-class {goCluster} | R Documentation

## Class "goCluster", a class for combining clustering results with functional annotation

### Description

This class provides a skeleton for the linkage of clustering results with statistical analysis of functional annotation.

### Objects from the Class

Objects can be created by calls of the form `new("goCluster")`.

### Slots

`data`:
  Object of class `"clusterData"`, the dataset that is going to be clustered.
`algo`:
  Object of class `"clusterAlgorithm"`, the algorithm that is used for clustering.
`sign`:
  Object of class `"clusterSignif"`, the function to estimate the significance of clusters based on the analysis of the associated annotation data.
`visu`:
  Object of class `"clusterVisual"`, which provides methods to visualize of the results.

### Methods

config
  `signature(object = "goCluster")`: interactive setup of the class.
setup
  `signature(object = "goCluster")`: returns the configuration as a list. This list can again be used for the non-interactive setup of the class.
setup<-
  `signature(object = "goCluster")`: non-interactive setup of the class. The option are specified using a list.
run
  `signature(object = "goCluster")`: run goCluster as specified during setup.
run<-
  `signature(object = "goCluster")`: run goCluster with the setting given as value to the assignment.
reset
  `signature(object = "goCluster")`: reset all results that were obtained during the last run of goCluster.
display
  `signature(object = "goCluster")`: calls the display function of the clusterVisual object defined for the goCluster anaylsis.
print
  `signature(object = "goCluster")`: calls the print function on each of the defined sub-objects. The output is being concatenated and returned to the user.

### Author(s)

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

### See Also

`clusterAnnotation-class`, `clusterData-class`, `clusterAlgorithm-class`, `clusterStatistic-class`, `clusterSignif-class`, `clusterVisual-class`, `config`, `setup`, `setup<-`, `execute`, `execute<-`, `reset` .

### Examples

    ## Load the configuration and create a new
    ## goCluster object
    data(benomylsetup)
    test <- new("goCluster")

    ## Perform the analysis by using the execute<- method
    execute(test) <- benomylsetup

[Package goCluster version 1.4.0 Index]