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 1.6.0 Index]