clusterAnnotationGO-abp-class {goCluster} | R Documentation

## Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.

### Description

This class can be used to reorganize the GO annotation from an AnnBuilder meta package to make it suitable for the statistical analysis.

### Details

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

### Slots

`meta`:
  Object of class `"character"`, specifies the `AnnBuilder` meta package which the class will use for the lookup of the initial GO IDs.
`trueid`:
  Object of class `"character"`, describes which unique ID has been used for building the annotation data package. This option is important in case your dataset is annotated with a different unique ID. In this case `goCluster` will have to convert the IDs of the dataset into the corresponding annotation IDs before removing duplicate entries.)
`uniqueid`:
  Object of class `"character"`, this is either a copy of the unique id of the parent data object (in case this is also the true ID) or a transformed vector according to the setting of the true ID.
`ontologies`:
  Object of class `"character"`, specifies one or several of the three GO ontologies that should be analyzed.
`evidence`:
  Object of class `"character"`, sets the evidence codes that are considered to be acceptable in the analysis.

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

### Extends

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

### Methods

config
  `signature(object = "clusterAnnotationGO")`: interactive setup of the class. You will be asked to specify the annotation package name and the sections of the gene ontology that you wish to include in your analysis. In addition unacceptable evidence codes can be excluded and the true linking ID can be specified.
setup
  `signature(object = "clusterAnnotationGO")`: 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 = "clusterAnnotationGO")`: non-interactive setup of the class. The options are specified using a list.
execute
  `signature(object = "clusterAnnotationGO")`: build the GO annotation information.
reset
  `signature(object = "clusterAnnotationGO")`: remove all annotation data that has been retrieved so that the `execute` function can be run again.
print
  `signature(object = "clusterAnnotationGO")`: 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

`prepareGOannotation`, `goCluster-class`, `clusterModule-class`, `clusterAnnotation-class`, `clusterData-class`

### Examples

    ## Predefined setup for goCluster
    data(benomylsetup)

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

    ## We only use the dataset from this object
    data <- test@data

    ## Get the annotation to the dataset
    testAnnotation <- execute(data@anno, test)

[Package goCluster version 1.4.0 Index]