clusterAnnotationGO-abp-class {goCluster} | R Documentation |
This class can be used to reorganize the GO annotation from an AnnBuilder meta package to make it suitable for the statistical analysis.
The class provides a wrapper around the prepareGOannotation
function. Please read the corresponding documentation for further
details.
meta
:"character"
,
specifies the AnnBuilder
meta package which the class will
use for the lookup of the initial GO IDs.trueid
:"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
:"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
:"character"
,
specifies one or several of the three GO ontologies that should be
analyzed.evidence
:"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
.
Class "clusterAnnotation"
, directly.
Class "clusterModule"
, by class "clusterAnnotation"
.
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.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. signature(object = "clusterAnnotationGO")
:
non-interactive setup of the class. The options are specified
using a list. signature(object = "clusterAnnotationGO")
:
build the GO annotation information.signature(object = "clusterAnnotationGO")
:
remove all annotation data that has been retrieved so that the
execute
function can be run again.signature(object = "clusterAnnotationGO")
:
This function prints some basic information about the content of
this object.Gunnar Wrobel, work@gunnarwrobel.de, http://www.gunnarwrobel.de.
prepareGOannotation
,
goCluster-class
,
clusterModule-class
,
clusterAnnotation-class
,
clusterData-class
## 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)