clusterSignifBonferroni-class {goCluster}R Documentation

Class "clusterSignifBonferroni"

Description

This class provides a selection mechanism that uses Bonferroni correction before selecting interesting annotation terms.

Details

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

Slots

threshold:
Object of class "numeric", the threshold for selecting interesting annotation terms. This threshold is applied to the Bonferroni corrected statistic and any terms with a p-value lower than the threshold will be returned.

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

Extends

Class "clusterSignif", directly. Class "clusterModule", by class "clusterSignif".

Methods

config
signature(object = "clusterSignifBonferroni"): interactive setup of the class. You can set the threshold here.
setup
signature(object = "clusterSignifBonferroni"): returns the configuration of the object as a list. This list can be used for the non-interactive setup of this class.
setup<-
signature(object = "clusterSignifBonferroni"): non-interactive setup of the class. You need to provide a list that contains the necessary settings for the class.
execute
signature(object = "clusterSignifBonferroni"): selects annotation terms that have a p-value lower than the given threshold.
reset
signature(object = "clusterSignifBonferroni"): resets the results of this class so that the selection process can be run again.

Author(s)

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

See Also

selectStatsBonferroni, goCluster-class, clusterSignif-class, clusterModule-class.

Examples

## FIXME: Add an example

[Package goCluster version 1.0.0 Index]