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A B C D E G I L M N O P R S T U misc
| %*%-method | Class "namedSparse" adds margin names to sparse matrices |
| %+% | Class "namedSparse" adds margin names to sparse matrices |
| +-method | Class "namedSparse" adds margin names to sparse matrices |
| A.csr | ~~data-name / kind ... |
| accessMat | matrix utilities for ontoTools. |
| accessMat-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| adjMat | Class "compoundGraph" list representation of multiple graph::graph |
| adjMat-method | Class "compoundGraph" list representation of multiple graph::graph |
| AMN | Class "namedSparse" adds margin names to sparse matrices |
| annoSource-class | Vocabulary for genomic data integration |
| annotationResource-class | Vocabulary for genomic data integration |
| Arith-method | Class "namedSparse" adds margin names to sparse matrices |
| as.matrix-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 |
| between-method | Class "compoundGraph" list representation of multiple graph::graph |
| 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-method | Class "taggedHierNomenclature" ~~~ |
| colinds | Class "namedSparse" adds margin names to sparse matrices |
| colinds-method | Class "namedSparse" adds margin names to sparse matrices |
| colSums | Class "namedSparse" adds margin names to sparse matrices |
| colSums-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 |
| conceptProbs | Compute semantic similarity measure for terms in an object-ontology |
| coverageMat | Class "OOC" object-ontology complex |
| coverageMat-method | Class "OOC" object-ontology complex |
| coverMat | matrix utilities for ontoTools. |
| DAG | Class "rootedDAG" |
| DAG-method | Class "rootedDAG" |
| daughterMat | matrix utilities for ontoTools. |
| daughterSpMat | matrix utilities for ontoTools. |
| depthStruct | tools for manipulating depth concepts for rooted DAGs |
| dimnames-method | Class "namedSparse" adds margin names to sparse matrices |
| dimnames<--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-method | Structures for working with formal nomenclatures |
| getMatrix | matrix utilities for ontoTools. |
| getMatrix-method | Class "rootedDAG" |
| getTerms | Structures for working with formal nomenclatures |
| getTerms-method | Vocabulary for genomic data integration |
| go1.15DAG | resources saved for computation of concept probabilities for GO MF |
| GOMF1.15 | resources saved for computation of concept probabilities for GO MF |
| gomfAmat | sparse matrix representing accessibilities of terms in GO MF graph; |
| goMFamat.1.15 | resources saved for computation of concept probabilities for GO MF |
| goMFamat.1.4 | resources saved for computation of concept probabilities for GO MF |
| goMFgraph.1.15 | resources saved for computation of concept probabilities for GO MF |
| goMFgraph.1.4 | resources saved for computation of concept probabilities for GO MF |
| goMFgraphDemo | sparse matrix representing accessibilities of terms in GO MF graph; |
| grep-method | Vocabulary for genomic data integration |
| grList | Class "compoundGraph" list representation of multiple graph::graph |
| grList-method | Class "compoundGraph" list representation of multiple graph::graph |
| Iyer517 | object-term mapping for human locuslink entries and GO MF |
| litObj | litOnto: graph illustrating the ontology concept; litObj: matrix |
| litOnto | litOnto: graph illustrating the ontology concept; litObj: matrix |
| LL2GOMFcp.1.15 | resources saved for computation of concept probabilities for GO MF |
| LL2GOMFcp.1.4 | resources saved for computation of concept probabilities for GO MF |
| LL2GOMFooc1.15 | resources saved for computation of concept probabilities for GO MF |
| LL2GOMFooMap.1.15 | resources saved for computation of concept probabilities for GO MF |
| LL2GOMFooMap.1.4 | resources saved for computation of concept probabilities for GO MF |
| LLGOMFcp | resources saved for computation of concept probabilities for GO MF |
| 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-method | Class "namedSparse" adds margin names to sparse matrices |
| maxval | Class "namedSparse" adds margin names to sparse matrices |
| maxval-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-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| namedSparse-class | Class "namedSparse" adds margin names to sparse matrices |
| ncol-method | Class "namedSparse" adds margin names to sparse matrices |
| newadj | matrix utilities for ontoTools. |
| nomenclature-class | Vocabulary for genomic data integration |
| nrow-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-class | Class "ontology" wraps a rooted DAG with some ontology metadata |
| ontology-method | Class "OOC" object-ontology complex |
| OOC-class | Class "OOC" object-ontology complex |
| OOmap | Class "OOC" object-ontology complex |
| OOmap-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-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| parents | Structures for working with formal nomenclatures |
| parents-method | Class "taggedHierNomenclature" ~~~ |
| pms | Compute semantic similarity measure for terms in an object-ontology |
| 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-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| revArcs | matrix utilities for ontoTools. |
| root | Class "rootedDAG" |
| root-method | Class "rootedDAG" |
| rootedDAG-class | Class "rootedDAG" |
| rowinds | Class "namedSparse" adds margin names to sparse matrices |
| rowinds-method | Class "namedSparse" adds margin names to sparse matrices |
| rowSums | Class "namedSparse" adds margin names to sparse matrices |
| rowSums-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 |
| SGDIvocab | Vocabulary for genomic data integration |
| show-method | Structures for working with formal nomenclatures |
| show-method | Class "OOC" object-ontology complex |
| show-method | Vocabulary for genomic data integration |
| show-method | Class "namedSparse" adds margin names to sparse matrices |
| show-method | Class "ontology" wraps a rooted DAG with some ontology metadata |
| show-method | Class "taggedHierNomenclature" ~~~ |
| STMA | Vocabulary from statistics theory and methods abstracts |
| subsumers | Compute semantic similarity measure for terms in an object-ontology |
| 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-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 |
| toDot-method | Class "compoundGraph" list representation of multiple graph::graph |
| toDot-method | Methods for Function toDot in Package 'ontoTools' - should be replaced |
| typedSymMapping-class | Vocabulary for genomic data integration |
| usageCount | Compute semantic similarity measure for terms in an object-ontology |
| [-method | Class "namedSparse" adds margin names to sparse matrices |