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A B C D E G I L M N O P R S T U misc
| %*%,namedSparse,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| %+% | Class "namedSparse" adds margin names to sparse matrices |
| +,namedSparse,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| A.csr | ~~data-name / kind ... |
| accessMat | matrix utilities for ontoTools. |
| accessMat,ontology-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| adjMat | Class "compoundGraph" list representation of multiple graph::graph objects |
| adjMat,compoundGraph-method | Class "compoundGraph" list representation of multiple graph::graph objects |
| AMN | Class "namedSparse" adds margin names to sparse matrices |
| annoSource-class | Vocabulary for genomic data integration |
| annotationResource-class | Vocabulary for genomic data integration |
| Arith,namedSparse,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| as.matrix,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| as.matrix.ok | Class "namedSparse" adds margin names to sparse matrices |
| between | Class "compoundGraph" list representation of multiple graph::graph objects |
| between,compoundGraph-method | Class "compoundGraph" list representation of multiple graph::graph objects |
| buildGOgraph | build graphNEL corresponding to bioc GO environment |
| child2parentMatDense | matrix utilities for ontoTools. |
| child2parentMatSparse | matrix utilities for ontoTools. |
| children | Structures for working with formal nomenclatures |
| children,character,taggedHierNomenclature-method | Class "taggedHierNomenclature" ~~~ |
| colinds | Class "namedSparse" adds margin names to sparse matrices |
| colinds,namedSparse,character-method | Class "namedSparse" adds margin names to sparse matrices |
| colSums | Class "namedSparse" adds margin names to sparse matrices |
| colSums,namedSparse,missing,missing-method | Class "namedSparse" adds margin names to sparse matrices |
| colSumsSp | Class "namedSparse" adds margin names to sparse matrices |
| compoundGraph-class | Class "compoundGraph" list representation of multiple graph::graph objects |
| conceptProbs | Compute semantic similarity measure for terms in an object-ontology complex |
| coverageMat | Class "OOC" object-ontology complex |
| coverageMat,OOC-method | Class "OOC" object-ontology complex |
| coverMat | matrix utilities for ontoTools. |
| DAG | Class "rootedDAG" |
| DAG,rootedDAG-method | Class "rootedDAG" |
| daughterMat | matrix utilities for ontoTools. |
| daughterSpMat | matrix utilities for ontoTools. |
| depthStruct | tools for manipulating depth concepts for rooted DAGs |
| dimnames,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| dimnames<-,namedSparse,list-method | Class "namedSparse" adds margin names to sparse matrices |
| DMdepth | tools for manipulating depth concepts for rooted DAGs |
| exns2 | Class "namedSparse" adds margin names to sparse matrices |
| exptArchive-class | Vocabulary for genomic data integration |
| exptSample-class | Vocabulary for genomic data integration |
| GDILabel | Structures for working with formal nomenclatures |
| GDILabel-class | Vocabulary for genomic data integration |
| GDIontology | Structures for working with formal nomenclatures |
| GDIontology-class | Vocabulary for genomic data integration |
| GDIplatform-class | Vocabulary for genomic data integration |
| GDI_NCIThesaurus | Structures for working with formal nomenclatures |
| getDefs | Structures for working with formal nomenclatures |
| getDefs,character,nomenclature-method | Structures for working with formal nomenclatures |
| getMatrix | matrix utilities for ontoTools. |
| getMatrix,rootedDAG,character,character-method | Class "rootedDAG" |
| getTerms | Structures for working with formal nomenclatures |
| getTerms,taggedHierNomenclature-method | Vocabulary for genomic data integration |
| go1.15DAG | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| GOMF1.15 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| gomfAmat | sparse matrix representing accessibilities of terms in GO MF graph; graph also documented here |
| goMFamat.1.15 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| goMFamat.1.4 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| goMFgraph.1.15 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| goMFgraph.1.4 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| goMFgraphDemo | sparse matrix representing accessibilities of terms in GO MF graph; graph also documented here |
| grep,character,taggedHierNomenclature-method | Vocabulary for genomic data integration |
| grList | Class "compoundGraph" list representation of multiple graph::graph objects |
| grList,compoundGraph-method | Class "compoundGraph" list representation of multiple graph::graph objects |
| Iyer517 | object-term mapping for human locuslink entries and GO MF |
| litObj | litOnto: graph illustrating the ontology concept; litObj: matrix illustrating the object-ontology mapping |
| litOnto | litOnto: graph illustrating the ontology concept; litObj: matrix illustrating the object-ontology mapping |
| LL2GOMFcp.1.15 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| LL2GOMFcp.1.4 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| LL2GOMFooc1.15 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| LL2GOMFooMap.1.15 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| LL2GOMFooMap.1.4 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| LLGOMFcp | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries |
| makeNamedSparse | Class "namedSparse" adds margin names to sparse matrices |
| makeOntology | Class "ontology" wraps a rooted DAG with some ontology metadata |
| makeOOC | Class "OOC" object-ontology complex |
| makeSparseZero | Class "namedSparse" adds margin names to sparse matrices |
| mapNamesInds | Class "namedSparse" adds margin names to sparse matrices |
| mat | Class "namedSparse" adds margin names to sparse matrices |
| mat,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| maxval | Class "namedSparse" adds margin names to sparse matrices |
| maxval,matrix.csr-method | Class "namedSparse" adds margin names to sparse matrices |
| mkNS | Class "namedSparse" adds margin names to sparse matrices |
| name | Class "ontology" wraps a rooted DAG with some ontology metadata |
| name,ontology-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| namedSparse-class | Class "namedSparse" adds margin names to sparse matrices |
| ncol,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| newadj | matrix utilities for ontoTools. |
| nomenclature-class | Vocabulary for genomic data integration |
| nrow,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| nsparse | Class "namedSparse" adds margin names to sparse matrices |
| ontoDepth | tools for manipulating depth concepts for rooted DAGs |
| ontology | Class "ontology" wraps a rooted DAG with some ontology metadata |
| ontology,OOC-method | Class "OOC" object-ontology complex |
| ontology-class | Class "ontology" wraps a rooted DAG with some ontology metadata |
| OOC-class | Class "OOC" object-ontology complex |
| OOmap | Class "OOC" object-ontology complex |
| OOmap,OOC-method | Class "OOC" object-ontology complex |
| ooMapLL2GOMFdemo | object-term mapping for human locuslink entries and GO MF |
| otkvEnv2namedSparse | obtain sparse matrix representation of key-value structures |
| otkvList2namedSparse | obtain sparse matrix representation of key-value structures |
| OVersion | Class "ontology" wraps a rooted DAG with some ontology metadata |
| OVersion,ontology-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| parents | Structures for working with formal nomenclatures |
| parents,character,taggedHierNomenclature-method | Class "taggedHierNomenclature" ~~~ |
| pms | Compute semantic similarity measure for terms in an object-ontology complex |
| provStruct | Structures for working with formal nomenclatures |
| provStruct-class | Vocabulary for genomic data integration |
| rDAG | Class "ontology" wraps a rooted DAG with some ontology metadata |
| rDAG,ontology-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| revArcs | matrix utilities for ontoTools. |
| root | Class "rootedDAG" |
| root,rootedDAG-method | Class "rootedDAG" |
| rootedDAG-class | Class "rootedDAG" |
| rowinds | Class "namedSparse" adds margin names to sparse matrices |
| rowinds,namedSparse,character-method | Class "namedSparse" adds margin names to sparse matrices |
| rowSums | Class "namedSparse" adds margin names to sparse matrices |
| rowSums,namedSparse,missing,missing-method | Class "namedSparse" adds margin names to sparse matrices |
| rowSumsSp | Class "namedSparse" adds margin names to sparse matrices |
| semsim | Compute semantic similarity measure for terms in an object-ontology complex |
| SGDIvocab | Vocabulary for genomic data integration |
| show,exptArchive-method | Vocabulary for genomic data integration |
| show,exptSample-method | Vocabulary for genomic data integration |
| show,GDIplatform-method | Vocabulary for genomic data integration |
| show,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| show,nomenclature-method | Structures for working with formal nomenclatures |
| show,ontology-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| show,OOC-method | Class "OOC" object-ontology complex |
| show,provStruct-method | Vocabulary for genomic data integration |
| show,symMapping-method | Vocabulary for genomic data integration |
| show,taggedHierNomenclature-method | Class "taggedHierNomenclature" ~~~ |
| STMA | Vocabulary from statistics theory and methods abstracts |
| subsumers | Compute semantic similarity measure for terms in an object-ontology complex |
| sumSp | Class "namedSparse" adds margin names to sparse matrices |
| sumSpSLOW | Class "namedSparse" adds margin names to sparse matrices |
| symMapping-class | Vocabulary for genomic data integration |
| t,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |
| taggedHierNomenclature | Class "taggedHierNomenclature" ~~~ |
| taggedHierNomenclature-class | Class "taggedHierNomenclature" ~~~ |
| thesList | Structures for working with formal nomenclatures |
| toDot | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,compoundGraph,character,list,list-method | Class "compoundGraph" list representation of multiple graph::graph objects |
| toDot,compoundGraph,character,list,missing-method | Class "compoundGraph" list representation of multiple graph::graph objects |
| toDot,compoundGraph,missing,list,missing-method | Class "compoundGraph" list representation of multiple graph::graph objects |
| toDot,graphNEL,character,list,list-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,graphNEL,character,missing,list-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,graphNEL,character,missing,missing-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,graphNEL,missing,character,missing-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,graphNEL,missing,list,list-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,graphNEL,missing,list,missing-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,graphNEL,missing,missing,list-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| toDot,graphNEL,missing,missing,missing-method | Methods for Function toDot in Package ‘ontoTools’ - should be replaced by Rgraphviz facilities soon |
| typedSymMapping-class | Vocabulary for genomic data integration |
| usageCount | Compute semantic similarity measure for terms in an object-ontology complex |
| [,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices |