OOC-class {ontoTools} | R Documentation |
Object that binds ontology (structured vocabulary) with an object-term map.
Objects can be created by calls of the form new("OOC", ...)
.
ontology
:"ontology"
instance of ontoTools::ontology OOmap
:"namedSparse"
SparseM::matrix.csr bound with dimnames facilities signature(x = "OOC")
: return a namedSparse
incidence matrix with r,c element indicating whether term c covers
object r signature(x = "OOC")
: accessor signature(x = "OOC")
: accessor signature(object = "OOC")
: concise printer VJ Carey <stvjc@channing.harvard.edu>
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