clusterData-class {goCluster}R Documentation

Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.

Description

This class provides a container for microarray data.

Details

This class provides a wrapper for exprSet objects from bioconductor. It provides a link to the annotation data in goCluster. A vector of unique ids that connects each element (row) in the dataset with its corresponding annotation terms has to be provided.

Slots

name:
Object of class "character", a name for the dataset.
dataset:
Object of class "exprSet", the dataset for the analysis.
uniqueid:
Object of class "character", the unique id for each gene (row) in the dataset.
anno:
Object of class "clusterAnnotation", the annotation object that holds the annotation to this dataset.

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

Extends

Class "clusterModule", directly.

Methods

config
signature(object = "clusterData"): interactive setup of the class.
setup
signature(object = "clusterData"): returns the configuration (including the dataset) of the object as a list. This list can be used for the non-interactive setup of the class.
setup<-
signature(object = "clusterData"): non-interactive setup of the class. The options are specified using a list.
execute
signature(object = "clusterData"): passes the execute-call to the annotation object.
execute<-
signature(object = "clusterData"): passes the execute<--call to the annotation object.
reset
signature(object = "clusterData"): This only conveys the reset signal to the clusterAnnotation object. The dataset of the clusterData object will not be removed by this reset method. A new goCluster-object should be created for each new dataset.
print
signature(object = "clusterData"): calls the print function of the exprSet-object stored in the dataset slot.

Author(s)

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

See Also

goCluster-class, clusterAnnotation-class, setup, setup<-, execute, reset.


[Package goCluster version 1.0.3 Index]