Entry: A.csr
Aliases: A.csr
Keywords: models
Description: ~~data-name / kind ...
URL: ../../../library/ontoTools/html/A.csr.html

Entry: GDI_NCIThesaurus
Aliases: GDI_NCIThesaurus thesList getDefs getTerms children parents GDIontology GDILabel provStruct show,nomenclature-method getDefs,character,nomenclature-method
Keywords: models
Description: Structures for working with formal nomenclatures
URL: ../../../library/ontoTools/html/GDI.html

Entry: LLGOMFcp
Aliases: LLGOMFcp LL2GOMFcp.1.4 LL2GOMFooMap.1.4 goMFamat.1.4 goMFgraph.1.4 LL2GOMFcp.1.15 LL2GOMFooc1.15 LL2GOMFooMap.1.15 goMFamat.1.15 goMFgraph.1.15 go1.15DAG GOMF1.15
Keywords: datasets
Description: resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries
URL: ../../../library/ontoTools/html/LLGOMFcp.html

Entry: OOC-class
Aliases: OOC-class OOmap coverageMat makeOOC OOmap,OOC-method show,OOC-method ontology,OOC-method coverageMat,OOC-method
Keywords: classes
Description: Class "OOC" object-ontology complex
URL: ../../../library/ontoTools/html/OOC-class.html

Entry: SGDIvocab
Aliases: SGDIvocab annoSource-class annotationResource-class exptArchive-class exptSample-class GDILabel-class GDIontology-class GDIplatform-class nomenclature-class provStruct-class symMapping-class typedSymMapping-class getTerms,taggedHierNomenclature-method grep,character,taggedHierNomenclature-method show,provStruct-method show,symMapping-method show,GDIplatform-method show,exptArchive-method show,exptSample-method
Keywords: models
Description: Vocabulary for genomic data integration
URL: ../../../library/ontoTools/html/SGDIvocab.html

Entry: STMA
Aliases: STMA
Keywords: models
Description: Vocabulary from statistics theory and methods abstracts
URL: ../../../library/ontoTools/html/STMA.html

Entry: accessMat
Aliases: accessMat child2parentMatDense child2parentMatSparse coverMat daughterSpMat daughterMat getMatrix newadj revArcs
Keywords: models
Description: matrix utilities for ontoTools.
URL: ../../../library/ontoTools/html/accessMat.html

Entry: buildGOgraph
Aliases: buildGOgraph
Keywords: models
Description: build graphNEL corresponding to bioc GO environment
URL: ../../../library/ontoTools/html/buildGOgraph.html

Entry: compoundGraph-class
Aliases: adjMat between grList compoundGraph-class adjMat,compoundGraph-method between,compoundGraph-method grList,compoundGraph-method toDot,compoundGraph,character,list,missing-method toDot,compoundGraph,character,list,list-method toDot,compoundGraph,missing,list,missing-method
Keywords: classes
Description: Class "compoundGraph" list representation of multiple graph::graph objects
URL: ../../../library/ontoTools/html/compoundGraph-class.html

Entry: depthStruct
Aliases: depthStruct DMdepth ontoDepth
Keywords: models
Description: tools for manipulating depth concepts for rooted DAGs
URL: ../../../library/ontoTools/html/depthStruct.html

Entry: gomfAmat
Aliases: gomfAmat goMFgraphDemo
Keywords: datasets
Description: sparse matrix representing accessibilities of terms in GO MF graph; graph also documented here
URL: ../../../library/ontoTools/html/gomfAmat.html

Entry: litOnto
Aliases: litOnto litObj
Keywords: datasets
Description: litOnto: graph illustrating the ontology concept; litObj: matrix illustrating the object-ontology mapping
URL: ../../../library/ontoTools/html/litOnto.html

Entry: namedSparse-class
Aliases: namedSparse-class colSums colSumsSp rowSums nsparse Arith,namedSparse,namedSparse-method [,namedSparse-method %*%,namedSparse,namedSparse-method +,namedSparse,namedSparse-method as.matrix,namedSparse-method colSums,namedSparse,missing,missing-method dimnames,namedSparse-method dimnames<-,namedSparse,list-method mat,namedSparse-method maxval,matrix.csr-method ncol,namedSparse-method nrow,namedSparse-method rowSums,namedSparse,missing,missing-method show,namedSparse-method t,namedSparse-method %+% AMN as.matrix.ok exns2 makeNamedSparse makeSparseZero mapNamesInds mat maxval mkNS rowSumsSp sumSp sumSpSLOW colinds,namedSparse,character-method rowinds,namedSparse,character-method rowinds colinds
Keywords: classes
Description: Class "namedSparse" adds margin names to sparse matrices
URL: ../../../library/ontoTools/html/namedSparse-class.html

Entry: ontology-class
Aliases: ontology-class ontology name OVersion name,ontology-method OVersion,ontology-method show,ontology-method makeOntology rDAG,ontology-method accessMat,ontology-method rDAG
Keywords: classes
Description: Class "ontology" wraps a rooted DAG with some ontology metadata
URL: ../../../library/ontoTools/html/ontology-class.html

Entry: ooMapLL2GOMFdemo
Aliases: ooMapLL2GOMFdemo Iyer517
Keywords: datasets
Description: object-term mapping for human locuslink entries and GO MF
URL: ../../../library/ontoTools/html/ooMapLL2GOMFdemo.html

Entry: otkvEnv2namedSparse
Aliases: otkvEnv2namedSparse otkvList2namedSparse
Keywords: models
Description: obtain sparse matrix representation of key-value structures
URL: ../../../library/ontoTools/html/otkvEnv2namedSparse.html

Entry: rootedDAG-class
Aliases: rootedDAG-class DAG root getMatrix,rootedDAG,character,character-method DAG,rootedDAG-method root,rootedDAG-method
Keywords: classes
Description: Class "rootedDAG"
URL: ../../../library/ontoTools/html/rootedDAG-class.html

Entry: semsim
Aliases: semsim pms subsumers conceptProbs usageCount
Keywords: models
Description: Compute semantic similarity measure for terms in an object-ontology complex
URL: ../../../library/ontoTools/html/semsim.html

Entry: taggedHierNomenclature-class
Aliases: taggedHierNomenclature-class taggedHierNomenclature children,character,taggedHierNomenclature-method parents,character,taggedHierNomenclature-method show,taggedHierNomenclature-method
Keywords: classes
Description: Class "taggedHierNomenclature" ~~~
URL: ../../../library/ontoTools/html/taggedHierNomenclature-class.html

Entry: toDot-methods
Aliases: toDot toDot,graphNEL,character,list,list-method toDot,graphNEL,character,missing,missing-method toDot,graphNEL,character,missing,list-method toDot,graphNEL,missing,missing,missing-method toDot,graphNEL,missing,missing,list-method toDot,graphNEL,missing,character,missing-method toDot,graphNEL,missing,list,list-method toDot,graphNEL,missing,list,missing-method
Keywords: methods
Description: Methods for Function toDot in Package 'ontoTools' -- should be replaced by Rgraphviz facilities soon
URL: ../../../library/ontoTools/html/toDot-methods.html
