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 |