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 1.0.9 Index]