\HeaderA{classificationModelSignalTrans}{Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components}{classificationModelSignalTrans}
\aliasA{modelSignalTrans}{classificationModelSignalTrans}{modelSignalTrans}
\keyword{datasets}{classificationModelSignalTrans}
\begin{Description}\relax
This file contains the hierarchical classification model to predict KEGG signaling pathways and pathway components for genes. The model contains only pathway components, to which a specified minimum number of genes could be mapped in the training phase (see \code{\LinkA{retrain.signaltrans}{retrain.signaltrans}}). Important: There exists one separate model file for each organism.
\end{Description}
\begin{Format}\relax
List of class "model", where each model has the following entries:
\describe{
\item[W] learned decision hyperplane normal vector
\item[C] dictionary of label vectors, which can be predicted individually or which can be used to predict combinations of them
\item[detectors] SVM models trained to separate one specific pathway branch from the rest of the hierarchy
\item[used\_domains] InterPro domains used by the classifier to separate the specific branch from the rest of the hierarchy
\item[alldomains] all InterPro domains used to build feature vectors
\item[allpathways] hierarchy branches, which can be predicted
\item[treesizes"] relative size of hierarchy below the corresponding branch
\item[kegg\_hierarchy] a nested list with information (parent branches, pathway names, pathway IDs, hierarchy level) on all higher hierarchy branches for each pathway
\item[elemIDs] a list of KEGG element IDs mapping to each pathway component -
may be used to highlight pathway components with
\code{\LinkA{color.pathway.by.elements}{color.pathway.by.elements}}.
}
\end{Format}
\begin{Author}\relax
Holger Froehlich
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{classificationModel}{classificationModel}}
\end{SeeAlso}

