# Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures

## Documentation for package ‘gene2pathway’ version 2.2.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

buildTrainingSet | internal functions
buildTrainingSet.signaltrans | internal functions
classificationModel | Hierarchical Classification Model
classificationModelSignalTrans | Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components
classificationModelSignalTrans_dme | Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components
classificationModelSignalTrans_hsa | Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components
classificationModel_dme | Hierarchical Classification Model
classificationModel_hsa | Hierarchical Classification Model
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
run.crossvalidation | Assessment of Prediction Performance via Cross-validation
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