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

Documentation for package ‘gene2pathway’ version 2.6.0

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

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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
classificationModelSignalTrans_dme	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
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
getInterProDomains	internal functions
getKEGGHierarchy	internal functions
internal	internal functions
loss	internal functions
modelKEGG	Hierarchical Classification Model
modelSignalTrans	Hierarchical Classification Model for Signaling Transduction Pathways and Pathway Components
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