Obtains a presenceabsence dependency matrix for the given set of terms. The resulting matrix M will have values 1 and 0, where M[i,j] = 1 iff the presence if term i implies the presence of term j. Note that it follows that M[i,j] = 1 iff the absence of term j implies the absence of term i. Note also that the matrix is asymmetric; that is, M[i,j] = 1 does not imply M[j,i] = 1 for \(i\neq j\). Terms i and j (\(i\neq j\)) for which M[i,j] = M[j,i] = 1 are sometimes referred to as superdependent.
pa_dep_matrix(terms, .names = c("ID", "IRI", "label"), .labels = NULL, preserveOrder = FALSE, verbose = FALSE)
terms  character, the list of terms for which to compute the dependency matrix. Can be given as term IRIs or term labels, and the list can contain both. Terms given as labels will first be resolved to IRIs, assuming they are from an anatomy ontology. 

.names  character, how to name the rows and columns of the resulting matrix.

.labels  character, the labels for terms where known. Only used if

preserveOrder  logical, whether to return rows (and columns) in the same
order as 
verbose  logical, whether to print informative messages about certain potentially timeconsuming operations. 
A data.fram M with M[i,j] = 1 iff the presence of term i implies the presence of term j, and 0 otherwise.
The matrix will have additional attributes depending on the choice of how to
name rows and columns. If .names = "ID"
(the default), the matrix will have
an attribute prefixes
giving the URL prefixes removed from the term IRIs
to yield the IDs, in the order of the rows. If .names = "label"
, it will
have attribute term.iris
, giving the term IRIs for the rows (and columns).
Note that these extra attributes will be lost upon subsetting the returned
matrix.
if (FALSE) { tl < c("http://purl.obolibrary.org/obo/UBERON_0000981", "http://purl.obolibrary.org/obo/UBERON_0002103", "http://purl.obolibrary.org/obo/UBERON_0000976", "http://purl.obolibrary.org/obo/UBERON_0002102") m < pa_dep_matrix(tl) m # term IDs as row and column names id_prefixes < attr(m, "prefixes") id_prefixes # 4x "http://purl.obolibrary.org/obo/" m < pa_dep_matrix(tl, .names = "label") m # term labels as row and column names mat_terms < attr(m, "term.iris") mat_terms # term IRIs in the same order as rows (and columns) }