# graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management

## Documentation for package `ontoTools' version 1.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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 --

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

## -- B --

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

## -- C --

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.

## -- D --

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

## -- E --

exns2 | Class "namedSparse" adds margin names to sparse matrices
exptArchive-class | Vocabulary for genomic data integration
exptSample-class | Vocabulary for genomic data integration

## -- G --

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
go1.5DAG | 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.1.4 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries
goMFamat.1.5 | 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
goMFgraph.1.5 | 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

## -- I --

Iyer517 | object-term mapping for human locuslink entries and GO MF

## -- L --

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.1.4 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries
LL2GOMFcp.1.5 | resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries
LL2GOMFooc1.5 | 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
LL2GOMFooMap.1.5 | 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

## -- M --

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

## -- N --

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

## -- O --

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

## -- P --

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

## -- R --

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

## -- S --

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 --

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

## -- U --

usageCount | Compute semantic similarity measure for terms in an object-ontology complex

## -- misc --

[,namedSparse-method | Class "namedSparse" adds margin names to sparse matrices