clusterAnnotationLookup-class {goCluster} | R Documentation

## Class "clusterAnnotationLookup", provides LocusLink -> GO annotation information via an external lookup table.

### Description

This class can be used to provide LocusLink IDs via a lookup table. The LocusLink ID's will then be mapped to GO identifiers.

### Details

The lookup file must have the common csv format. It must provide a header with the column names and the values are seperated by ",". The file may only have two columns. The first column specifies the locus link ID, the second column represents the matching gene ID. Please ensure that the gene ID's do match exactly to the rownames in your dataset.

While this class only links LocusLink with Go it is actually a good example of how you can import external data from a lookup table into the statistical analysis process of goCluster.

### Slots

`lookup`:
  Path to the lookup table.

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 = "clusterAnnotationLookup")`: interactive setup of the class. You will be asked to specify the path of the lookup file.
setup
  `signature(object = "clusterAnnotationLookup")`: 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 = "clusterAnnotationLookup")`: build the annotation information to make it suitable for statistical analysis.
reset
  `signature(object = "clusterAnnotationLookup")`: remove all annotation data that has been retrieved so that the `execute` function can be run again.
print
  `signature(object = "clusterAnnotationLookup")`: 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

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

### Examples

[Package goCluster version 1.6.0 Index]