GOTerms-class         package:AnnotationDbi         R Documentation

_C_l_a_s_s "_G_O_T_e_r_m_s"

_D_e_s_c_r_i_p_t_i_o_n:

     A class to represent Gene Ontology nodes

_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 'GOTerms(GOId, term,
     ontology, definition, synonym, secondary)'. GOId, term, and
     ontology are required.

_S_l_o_t_s:

     '_G_O_I_D': Object of class '"character"' A character string for the
          GO id of a primary node.

     '_T_e_r_m': Object of class '"character"' A character string that
          defines the role of gene product corresponding to the primary
          GO id.

     '_O_n_t_o_l_o_g_y': Object of class '"character"' Gene Ontology category.
          Can be MF - molecular function, CC - cellular component, or
          BP - biological process.

     '_D_e_f_i_n_i_t_i_o_n': Object of class '"character"' Further definition of
          the ontology of the primary GO id.

     '_S_y_n_o_n_y_m': Object of class '"character"' other ontology terms that
          are considered to be synonymous to the primary term attached
          to the GO id (e.g. "type I programmed cell death" is a
          synonym of "apoptosis"). Synonymous here can mean that the
          synonym is an exact synonym of the primary term, is related
          to the primary term, is broader than the primary term, is
          more precise than the primary term, or name is related to the
          term, but is not exact, broader or narrower.

     '_S_e_c_o_n_d_a_r_y': Object of class '"character"' GO ids that are
          secondary to the primary GO id as results of merging GO terms
          so that One GO id becomes the primary GO id and the rest
          become the secondary.

_M_e_t_h_o_d_s:

     _G_O_I_D 'signature(object = "GOTerms")': The get method for slot
          GOID.

     _T_e_r_m 'signature(object = "GOTerms")': The get method for slot
          Term.

     _O_n_t_o_l_o_g_y 'signature(object = "GOTerms")': The get method for slot
          Ontology.

     _D_e_f_i_n_i_t_i_o_n 'signature(object = "GOTerms")': The get method for
          slot Definition.

     _S_y_n_o_n_y_m 'signature(object = "GOTerms")': The get method for slot
          Synonym.

     _S_e_c_o_n_d_a_r_y 'signature(object = "GOTerms")': The get method for slot
          Secondary.

     _s_h_o_w 'signature(x = "GOTerms")': The method for pretty print.

_N_o_t_e:

     GOTerms objects are used to represent primary GO nodes in the
     SQLite-based annotation data package GO.db

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.geneontology.org/>

_E_x_a_m_p_l_e_s:

       gonode <- new("GOTerms", GOID="GO:1234567", Term="Test", Ontology="MF",
                               Definition="just for testing")
       GOID(gonode)
       Term(gonode)
       Ontology(gonode)

