OOC-class             package:ontoTools             R Documentation

_C_l_a_s_s "_O_O_C" _o_b_j_e_c_t-_o_n_t_o_l_o_g_y _c_o_m_p_l_e_x

_D_e_s_c_r_i_p_t_i_o_n:

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

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

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

_S_l_o_t_s:

     '_o_n_t_o_l_o_g_y': Object of class '"ontology"' instance of
          ontoTools::ontology 

     '_O_O_m_a_p': Object of class '"namedSparse"' SparseM::matrix.csr bound
          with dimnames facilities 

_M_e_t_h_o_d_s:

     _c_o_v_e_r_a_g_e_M_a_t 'signature(x = "OOC")': return a namedSparse incidence
          matrix with r,c element indicating whether term c covers
          object r  

     _o_n_t_o_l_o_g_y 'signature(x = "OOC")': accessor 

     _O_O_m_a_p 'signature(x = "OOC")': accessor 

     _s_h_o_w 'signature(object = "OOC")': concise printer 

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     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

