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]