clusterAnnotationChromosome-abp-class {goCluster} | R Documentation |
This class can be used to retrieve the chromosome
information for subsequent use in a goCluster
-analysis.
The class provides a wrapper around the prepareCHRannotation
function. Please read the corresponding documentation for further
details.
meta
:"character"
,
specifies the AnnBuilder meta package that the class will use for
the lookup of chromosome information.trueid
:"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
:"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
:"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
.
Class "clusterAnnotation"
, directly.
Class "clusterModule"
, by class "clusterAnnotation"
.
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.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. signature(object = "clusterAnnotationChromosome")
:
non-interactive setup of the class. The options are specified
using a list. signature(object = "clusterAnnotationChromosome")
:
build the chromosome annotation information.signature(object = "clusterAnnotationChromosome")
:
remove all annotation data that has been retrieved so that the
execute
function can be run again.signature(object = "clusterAnnotationChromosome")
:
This function prints some basic information about the content of
this object.Gunnar Wrobel, work@gunnarwrobel.de, http://www.gunnarwrobel.de.
prepareCHRannotation
,
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 ## 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)