clusterAnnotationChromosome-abp-class {goCluster} | R Documentation

## Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.

### Description

This class can be used to retrieve the chromosome information for subsequent use in a `goCluster`-analysis.

### Details

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

### Slots

`meta`:
  Object of class `"character"`, specifies the AnnBuilder meta package that the class will use for the lookup of chromosome information.
`trueid`:
  Object of class `"character"`, describes which id has actually been used for the building of the annotation package (this is important for some of the AnnBuilder packages that use LocusLink as central ID.
`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.
`chromosomes`:
  Object of class `"character"`, this can be used to limit the analysis to specific chromosomes.

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

`prepareCHRannotation`, `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

    ## The predefined configuration is set to retrieve the
    ## gene ontology information. We need to exchange this
    ## with chromosome annotation
    anno <- new("clusterAnnotationChromosome-abp")
    setup(anno) <- list(meta = "YEAST",
                        chromosomes = as.character(seq(1:16)),
                        trueid = "")
    data@anno <- anno

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

[Package goCluster version 1.6.0 Index]