Package 'BioMVCClass'

Class "exprModel": A class to represent an ExpressionSet model

Description

exprModel is a class to represent an ExpresssionSet model. This class inherits from the virtual class, gModel. An object of exprModel is responsible for storing and updating the data.

Objects from the Class

Objects can be created by calls of the form new("exprModel", ...). The initialize method for this class will be created in other packages that use this package (for example, the initialize method will be created in the iSNetwork package).

Slots

modelData:

the model data, which is an ExpressionSet

linkData:

a list of functions that link this model to its parent and child models (if it has any)

virtualData:

the data that is needed by the views of this object

modelName:

the name of this model

modelVar:

a list of variables that refer to the modelData (for instance this may be t-test values that were calculated from the modelData)

Extends

Class "gModel", directly.

Methods

No methods defined with class "exprModel" in the signature. The methods for this class will be created in other packages that use this package like iSNetwork.

Author(s)

Elizabeth Whalen

See Also

graphModel-class

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Class "graphModel": A class to represent a graph model

Description

graphModel is a class to represent a graph model. This class inherits from the virtual class, gModel. An object of graphModel is responsible for storing and updating the data.

Objects from the Class

Objects can be created by calls of the form new("graphModel", ...). The initialize method for this class will be created in other packages that use this package (for example, the initialize method will be created in the iSNetwork package).

Slots

modelData:

the model data, which is a graph object

linkData:

a list of functions that link this model to its parent and child models (if it has any)

virtualData:

data that is needed by views of this model

modelName:

the name of this model

modelVar:

a list of variables that refer to the modelData (for instance this may be t-test values that were calculated from the modelData)

Extends

Class "gModel", directly.

Methods

No methods defined with class "graphModel" in the signature. The methods for this class will be created in other packages that use this package like iSNetwork.

Author(s)

Elizabeth Whalen

See Also

exprModel-class

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Class "graphView": A class to represent a graph view

Description

graphView is a class to represent a view that is a graph. graphView inherits from the class, plotView, which inherits from the virtual class, genView.

Objects from the Class

Objects can be created by calls of the form new("graphView", ...). The initialize method for this class will be created in other packages that use this package (for example, the initialize method will be created in the iSNetwork package).

Slots

plotDevice:

the plot device number

plotPar:

the parameter list for the plot, see par()

drArea:

an object of class "GtkDrawingArea"

dataName:

a character string describing what data are shown in the view

win:

an object of class "GtkWindow" that holds the view

winNum:

a number that tells what number view this is (for example, the first view created will have winNum=1)

grLayout:

the Ragraph object, which represents the layout for the graph plot

Extends

Class "plotView", directly. Class "genView", by class "plotView".

Methods

No methods defined with class "graphView" in the signature.

Author(s)

Elizabeth Whalen

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Class "GSE": A class to represent gene set enrichment data

Description

GSE is a class to represent gene set enrichment data and will be used in the modelData slot in the gseModel object. This class will store all of the information that pertains to performing gene set enrichment.

Objects from the Class

Objects can be created by calls of the form new("GSE", ...).

Slots

incidMat:

the incidence matrix that shows the relationship between the genes and the gene sets

gTestStat:

the test statistic for the genes relationship with the phenotype

gsTestStat:

the test statistic for the gene set

expData:

the experimental data (here it will be of class ExpressionSet)

descr:

a description of the gene set being studied

Methods

incidMat<-

Sets the incidMat slot

incidMat

Returns the incidMat slot

gTestStat<-

Sets the gTestStat slot

gTestStat

Returns the gTestStat slot

gsTestStat<-

Sets the gsTestStat slot

gsTestStat

Returns the gsTestStat slot

expData<-

Sets the expData slot

expData

Returns the expData slot

descr<-

Sets the descr slot

descr

Returns the descr slot

Author(s)

Elizabeth Whalen

See Also

gseModel-class

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Class "gseModel": A class to represent a GSE model

Description

gseModel is a class to represent a gene set enrichment (GSE) model. This class inherits from the virtual class, gModel.

Objects from the Class

Objects can be created by calls of the form new("gseModel", ...). The initialize method for this class will be created in other packages that use this package (for example, the initialize method will be created in the iSNetwork package).

Slots

modelData:

the model data, which is an object of GSE

linkData:

a list of functions that link this model to its parent and child models (if it has any)

virtualData:

the data that is needed by the views of this object

modelName:

the name of this model

modelVar:

a list of variables that refer to the modelData (for instance this may be t-test values that were calculated from the modelData)

Extends

Class "gModel", directly.

Methods

No methods defined with class "gseModel" in the signature. The methods for this class will be created in other packages that use this package like iSNetwork.

Author(s)

Elizabeth Whalen

See Also

GSE-class, graphModel-class, exprModel-class

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Class "heatmapView": A class to represent a heatmap view

Description

heatmapView is a class to represent a view that is a heatmap. heatmapView inherits from the class, plotView, which inherits from the virtual class, genView.

Objects from the Class

Objects can be created by calls of the form new("heatmapView", ...). The initialize method for this class will be created in other packages that use this package (for example, the initialize method will be created in the iSNetwork package).

Slots

ordering:

a list of of information returned from the heatmap function

plotDevice:

the plot device number

plotPar:

the parameter list for the plot, see par()

drArea:

an object of class "GtkDrawingArea"

dataName:

a character string describing what data are shown in the view

win:

an object of class "GtkWindow" that holds the view

winNum:

a number that tells what number view this is (for example, the first view created will have winNum=1)

rNames:

the names of the rows to be included in the heatmap (this allows the original data to be subset in the view)

Extends

Class "plotView", directly. Class "genView", by class "plotView".

Methods

ordering<-

Sets the ordering slot

ordering

Returns the ordering slot

rNames<-

Sets the rNames slot

rNames

Returns the rNames slot

Author(s)

Elizabeth Whalen

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