graphs and sparse matrices for working with ontologies


[Package List] [Top]

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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.
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

-- G --

getMatrix matrix utilities for ontoTools.
getMatrix,rootedDAG,character,character-method Class "rootedDAG"
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
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
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.
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"
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
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 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

-- U --

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

-- misc --

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