A subsumer matrix M for terms \(j \in \{1, \dots, n\}\) has value \(M_{i,j}=1\) iff class i (which can be an anonymous class expression) subsumes term j, and zero otherwise. Therefore, it will have n columns, one for each term.
subsumer_matrix(terms, .colnames = 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. 

.colnames  character, how to name the columns of the resulting matrix.

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

preserveOrder  logical, whether to return columns in the same
order as 
verbose  logical, whether to print informative messages about certain potentially timeconsuming operations. 
A data.frame representing the subsumer matrix
The matrix will have additional attributes depending on the choice of how to
name rows and columns. If .colnames = "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 .colnames = "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.
In this implementation, for each row i \(\sum_{j=1}^{n}M_{i,j} > 0\). That is, each row will have at least one nonzero value, which means that the number of classes not subsuming a term will be highly incomplete, because the (usually very many) classes not subsuming any of the terms will not be included. This subsumer matrix is thus only useful for similarity metrics for which nonsubsuming terms can be ignored.
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 < subsumer_matrix(tl) m < # term IDs as column names id_prefixes < attr(m, "prefixes") id_prefixes # 4x "http://purl.obolibrary.org/obo/" m < subsumer_matrix(tl, .colnames = "label") m # term labels as column names mat_terms < attr(m, "term.iris") mat_terms # term IRIs in the same order as columns }