OOC-class {ontoTools}R Documentation

Class "OOC" object-ontology complex

Description

Object that binds ontology (structured vocabulary) with an object-term map.

Objects from the Class

Objects can be created by calls of the form new("OOC", ...).

Slots

ontology:
Object of class "ontology" instance of ontoTools::ontology
OOmap:
Object of class "namedSparse" SparseM::matrix.csr bound with dimnames facilities

Methods

coverageMat
signature(x = "OOC"): return a namedSparse incidence matrix with r,c element indicating whether term c covers object r
ontology
signature(x = "OOC"): accessor
OOmap
signature(x = "OOC"): accessor
show
signature(object = "OOC"): concise printer

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples

data(litOnto)
g1 <- new("rootedDAG", DAG=litOnto, root="A")
o1 <- new("ontology", name="demo", version="0.1",
        rDAG=g1)
kvlist <- list(W="E", X="K", Y="B", Z=c("D","G"))
litMap <- otkvList2namedSparse( names(kvlist), LETTERS[1:12], kvlist )
print(litMap)
ooc1 <- makeOOC( o1, litMap )
show(ooc1)
print(coverageMat(ooc1))
# note the following will be slow with large OOCs
print(conceptProbs(ooc1))
# for larger OOCs it is useful to precompute the accessibility
# matrix of the ontology and the map from objects to terms -- these
# can be supplied as additional arguments to conceptProbs

[Package ontoTools version 1.6.0 Index]