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


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Documentation for package ‘gene2pathway’ version 2.2.0

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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
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