stamNode-class {stam}R Documentation

Nodes in a Classifier Net by StAM

Description

Objects of this class and its subclasses represent single nodes in a classifier net as it is used by structured analysis of microarray data.

Objects from the Classes

Objects can be created by calls of the form new("stamNode", ID, supNode).

ID
is the GO identifier as character string
supNode
indicates whether the node is a supplementary node to avoid nodes which have both, genes directly annotated and children in the stamNet.

Slots

ID:
Object of class "character", holds the GO identifier as character string
category:
Object of class "character", represents the GO ontology the node belongs (MF: molecular function, BP: biological process, CC: cellular component).
replacedParents:
Object of class "character", holds all GO identifiers of nodes which have been removed, because the had only one child.
supNode:
Object of class "logical", indicates whether the nodes has been added to avoid nodes which have both directly annotated genes as well as children in the classifier graph

Methods

getGOchildren
signature(x = "stamNode"): returns the identifiers of the direct children of node x in the Gene Ontology.
getGOchildren
signature(x = "character"): returns the identifiers of the direct children of the node with identifier x in the Gene Ontology.
getGOparents
signature(x = "stamNode"): returns the identifiers of the direct parents of node x in the Gene Ontology.
getGOparents
signature(x = "character"): returns the identifiers of the direct parents of the node with identifier x in the Gene Ontology.
getGOterm
signature(x = "stamNode"): returns the GO term represented by node x.
getGOterm
signature(x = "character"): returns the GO term represented by the node with identifier x.
print
signature(x = "stamNode") print information on the node.
writeHTML
signature(x = "stamNode") generate HTML information on the node.

Author(s)

Claudio Lottaz

See Also

stamLeaf-class, stamINode-class


[Package stam version 1.0.3 Index]