| 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,ANY,ANY,ANY,ANY,ANY,ANY,missing-method |
Vocabulary for genomic data integration |
| 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 |
| 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 |
| 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 |