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 |