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

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Documentation for package ‘ontoTools’ version 1.32.0

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A B C D E G I L M N O P R S T U misc

-- A --

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 objects
adjMat-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-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

-- B --

between Class "compoundGraph" list representation of multiple graph::graph objects
between-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-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 objects
conceptProbs Compute semantic similarity measure for terms in an object-ontology complex
coverageMat Class "OOC" object-ontology complex
coverageMat-method Class "OOC" object-ontology complex
coverMat matrix utilities for ontoTools.

-- D --

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

-- 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-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 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-method Vocabulary for genomic data integration
grList Class "compoundGraph" list representation of multiple graph::graph objects
grList-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.1.15 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

-- 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-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

-- N --

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

-- O --

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

-- P --

parents Structures for working with formal nomenclatures
parents-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-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

-- S --

semsim Compute semantic similarity measure for terms in an object-ontology complex
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 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-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-method Class "compoundGraph" list representation of multiple graph::graph objects
toDot-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 --

%*%-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
[-method Class "namedSparse" adds margin names to sparse matrices