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)

