GOTerms-class            package:annotate            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 terms for a given node

_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("GOTerms", GOId,
     Term, Category, Synonym, Secondary, Definition)'. GOId, Term, and
     Category are required.

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

     '_G_O_I_D': Object of class '"character"' A character stirng 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

     '_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

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

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

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

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

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

     _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

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

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

     _p_r_i_n_t 'signature(x = "GOTerms")': The method for pretty print

_N_o_t_e:

     GOTerms objects are used to represent GO terms for primary GO
     nodes in the annotation data package GO

_A_u_t_h_o_r(_s):

     Jianhua Zhang

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

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

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

       goTerms <- new("GOTerms", GOID = "GO:1234567", Term = "Test",
                      Ontology = "MF")
       GOID(goTerms)
       Term(goTerms)
       Ontology(goTerms)

