clusterAnnotationLookup-class {goCluster} | R Documentation |
This class can be used to provide LocusLink IDs via a lookup table. The LocusLink ID's will then be mapped to GO identifiers.
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.
lookup
:
Additional slots are described in the documentation of the
clusterAnnotation-class
and clusterModule-class
.
Class "clusterAnnotation"
, directly.
Class "clusterModule"
, by class "clusterAnnotation"
.
signature(object = "clusterAnnotationLookup")
:
interactive setup of the class. You will be asked to specify the
path of the lookup file.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. signature(object = "clusterAnnotationGO")
:
non-interactive setup of the class. The options are specified
using a list. signature(object = "clusterAnnotationLookup")
:
build the annotation information to make it suitable for
statistical analysis.signature(object = "clusterAnnotationLookup")
:
remove all annotation data that has been retrieved so that the
execute
function can be run again.signature(object = "clusterAnnotationLookup")
:
This function prints some basic information about the content of
this object.Gunnar Wrobel, work@gunnarwrobel.de, http://www.gunnarwrobel.de.
goCluster-class
,
clusterModule-class
,
clusterAnnotation-class
,
clusterData-class