classificationModel {gene2pathway} | R Documentation |
Hierarchical Classification Model
Description
This file contains the hierarchical classification model to predict KEGG pathway branches for genes. The model uses a pruned KEGG hierarchy, where metabolic pathways are not distinguished further, and the KEGG hierarchy for "cellular processes" and "genetic information processing" is pruned at the 2nd level. By default the model uses bagging to improve prediction accuracy. Important: There exists one separate model file for each organism.
Format
List of class "model", where each model has the following entries:
Wlearned decision hyperplane normal vector
Cdictionary of label vectors, which can be predicted individually or which can be used to predict combinations of them
detectorsSVM models trained to separate one specific pathway branch from the rest of the hierarchy
used_domainsInterPro domains used by the classifier to separate the specific branch from the rest of the hierarchy
alldomainsall InterPro domains used to build feature vectors
allpathwayshierarchy branches, which can be predicted
treesizesrelative size of hierarchy below the corresponding branch
parentPathsa list with information on all higher hierarchy branches for each pathway
Author(s)
Holger Froehlich
See Also
classificationModelSignalTrans
[Package
gene2pathway version 1.0
Index]