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| buildTrainingSet | internal functions |
| buildTrainingSet.signaltrans | internal functions |
| classificationModel | Hierarchical Classification Model |
| classificationModelSignalTrans | Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components |
| code_test | internal functions |
| code_train | internal functions |
| color.pathway.by.elements | KEGG pathway information |
| Entrez2ORF | Conversion locus tag -> Entrez ID and Entrez ID -> locus tag according to KEGG |
| Entrez2ORF.internal | internal functions |
| gene2pathway | Pathway membership prediction |
| gene2pathway.signaltrans | Pathway membership prediction |
| get.element.relations.by.pathway | internal functions |
| get.elements.by.pathway | KEGG pathway information |
| getComponents | KEGG pathway information |
| getComponents.internal | internal functions |
| getInterProDomains | internal functions |
| getKEGGHierarchy | internal functions |
| internal | internal functions |
| KEGG2Entrez | internal functions |
| loss | internal functions |
| modelKEGG | Hierarchical Classification Model |
| modelSignalTrans | Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components |
| ORF2Entrez | Conversion locus tag -> Entrez ID and Entrez ID -> locus tag according to KEGG |
| predict.gene2pathway | internal functions |
| retrain | Retrain classification model |
| retrain.signaltrans | Retrain classification model for signaling pathways |
| struct_predict | internal functions |
| struct_train | internal functions |
| svmlearn | internal functions |
| svmpredict | internal functions |
| test.overrepresentation | Test statistical overrepresentation of KEGG pathways in a list of genes |