graphs and sparse matrices for working with ontologies


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A B C D E G 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
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.
colindex Class "namedSparse" adds margin names to sparse matrices
colindex,namedSparse-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 matrix utilities for ontoTools.
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 --

exns Class "namedSparse" adds margin names to sparse matrices

-- G --

getMatrix matrix utilities for ontoTools.
getMatrix,rootedDAG,character,character-method Class "rootedDAG"
gomfAmat sparse matrix representing accessibilities of terms in GO MF graph; graph also documented here
goMFgraphDemo sparse matrix representing accessibilities of terms in GO MF graph; graph also documented here
grList Class "compoundGraph" list representation of multiple graph::graph objects
grList,compoundGraph-method Class "compoundGraph" list representation of multiple graph::graph objects

-- 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
LLGOMFcp 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
multiget 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.
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 --

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

-- 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"
rowindex Class "namedSparse" adds margin names to sparse matrices
rowindex,namedSparse-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
show,namedSparse-method Class "namedSparse" adds margin names to sparse matrices
show,ontology-method Class "ontology" wraps a rooted DAG with some ontology metadata
show,OOC-method Class "OOC" object-ontology complex
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

-- T --

t,namedSparse-method Class "namedSparse" adds margin names to sparse matrices
toDot Class "compoundGraph" list representation of multiple graph::graph objects
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
toDot-methods Methods for Function toDot in Package `ontoTools' - should be replaced by Rgraphviz facilities soon

-- U --

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

-- misc --

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