clusterSignifBase-class {goCluster} | R Documentation |
This class provides a very simple selection mechanism to identify interesting annotation terms.
The class provides a wrapper around the selectStats
function. Please read the corresponding documentation for further
details.
threshold
:"numeric"
, the
threshold for selecting interesting annotation terms. This
threshold is applied to the statistic returned by the
clusterStatistic
-class and any terms with a p-value
lower than the threshold will be returned.
Additional slots are described in the documentation of the
clusterSignif-class
and clusterModule-class
.
Class "clusterSignif"
, directly.
Class "clusterModule"
, by class "clusterSignif"
.
signature(object = "clusterSignifBase")
:
interactive setup of the class. You can set the threshold here.signature(object = "clusterSignifBase")
:
returns the configuration of the object as a list. This list can
be used for the non-interactive setup of this class. signature(object = "clusterSignifBase")
:
non-interactive setup of the class. You need to provide a list
that contains the necessary settings for the class. signature(object = "clusterSignifBase")
:
selects annotation terms that have a p-value lower than the given
threshold. signature(object = "clusterSignifBase")
:
resets the results of this class so that the selection process can
be run again. signature(object = "clusterSignifBase")
:
This function prints some basic information about the content of
this object. If the object has been executed, it will show the
number of identified annotation terms. Gunnar Wrobel, work@gunnarwrobel.de, http://www.gunnarwrobel.de.
selectStats
,
goCluster-class
,
clusterSignif-class
,
clusterModule-class
## Load a small test dataset data(benomylsetupsmall) ## Create an emty goCluster object test <- new("goCluster") ## Modify the configuration to use this significance class benomylsetupsmall$classsign <- "clusterSignifBase" ## Assign the configuration to the object and directly execute it execute(test) <- benomylsetupsmall ## This should show you the selected annotations. They should ## all have a value below 0.05. test@sign@selection