\HeaderA{stamNode-class}{Nodes in a Classifier Net by StAM}{stamNode.Rdash.class}
\aliasA{getGOchildren,character-method}{stamNode-class}{getGOchildren,character.Rdash.method}
\aliasA{getGOchildren,stamNode-method}{stamNode-class}{getGOchildren,stamNode.Rdash.method}
\aliasA{getGOparents,character-method}{stamNode-class}{getGOparents,character.Rdash.method}
\aliasA{getGOparents,stamNode-method}{stamNode-class}{getGOparents,stamNode.Rdash.method}
\aliasA{getGOterm,character-method}{stamNode-class}{getGOterm,character.Rdash.method}
\aliasA{getGOterm,stamNode-method}{stamNode-class}{getGOterm,stamNode.Rdash.method}
\aliasA{initialize,stamNode-method}{stamNode-class}{initialize,stamNode.Rdash.method}
\aliasA{print,stamNode-method}{stamNode-class}{print,stamNode.Rdash.method}
\aliasA{writeHTML,stamNode-method}{stamNode-class}{writeHTML,stamNode.Rdash.method}
\keyword{classes}{stamNode-class}
\begin{Description}\relax
Objects of this class and its subclasses represent single nodes in a classifier net as
it is used by structured analysis of microarray data.
\end{Description}
\begin{Section}{Objects from the Classes}
Objects can be created by calls of the form \code{new("stamNode", ID, supNode)}.
\item[ID] is the GO identifier as character string
\item[supNode] indicates whether the node is a supplementary node to avoid nodes which 
have both, genes directly annotated and children in the stamNet.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{ID}:] Object of class \code{"character"}, holds the GO identifier as 
character string
\item[\code{category}:] Object of class \code{"character"}, represents the GO 
ontology the node belongs (MF: molecular function, BP: biological process, CC: 
cellular component).
\item[\code{replacedParents}:] Object of class \code{"character"}, holds all GO 
identifiers of nodes which have been removed, because the had only one child.
\item[\code{supNode}:] Object of class \code{"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
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[getGOchildren] \code{signature(x = "stamNode")}: returns the identifiers of the
direct children of node x in the Gene Ontology.
\item[getGOchildren] \code{signature(x = "character")}: returns the identifiers of 
the direct children of the node with identifier x in the Gene Ontology.
\item[getGOparents] \code{signature(x = "stamNode")}: returns the identifiers of the
direct parents of node x in the Gene Ontology.
\item[getGOparents] \code{signature(x = "character")}: returns the identifiers of the
direct parents of the node with identifier x in the Gene Ontology.
\item[getGOterm] \code{signature(x = "stamNode")}: returns the GO term represented by
node x.
\item[getGOterm] \code{signature(x = "character")}: returns the GO term represented by
the node with identifier x.
\item[print] \code{signature(x = "stamNode")} print information on the node.
\item[writeHTML] \code{signature(x = "stamNode")} generate HTML information on the 
node.
}
\end{Section}
\begin{Author}\relax
Claudio Lottaz
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{stamLeaf-class}{stamLeaf.Rdash.class}}, \code{\LinkA{stamINode-class}{stamINode.Rdash.class}}
\end{SeeAlso}

