classificationModelSignalTrans {gene2pathway} | R Documentation |
Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components
Description
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 retrain.signaltrans
). Important: There exists one separate model file for each organism.
Format
List of class "model", where each model has the following entries:
- W
- learned decision hyperplane normal vector
- C
- dictionary of label vectors, which can be predicted individually or which can be used to predict combinations of them
- detectors
- SVM models trained to separate one specific pathway branch from the rest of the hierarchy
- used_domains
- InterPro domains used by the classifier to separate the specific branch from the rest of the hierarchy
- alldomains
- all InterPro domains used to build feature vectors
- allpathways
- hierarchy branches, which can be predicted
- treesizes"
- relative size of hierarchy below the corresponding branch
- kegg_hierarchy
- a nested list with information (parent branches, pathway names, pathway IDs, hierarchy level) on all higher hierarchy branches for each pathway
- elemIDs
- a list of KEGG element IDs mapping to each pathway component -
may be used to highlight pathway components with
color.pathway.by.elements
.
Author(s)
Holger Froehlich
See Also
classificationModel
[Package
gene2pathway version 1.2.0
Index]