stamNode-class             package:stam             R Documentation

_N_o_d_e_s _i_n _a _C_l_a_s_s_i_f_i_e_r _N_e_t _b_y _S_t_A_M

_D_e_s_c_r_i_p_t_i_o_n:

     Objects of this class and its subclasses represent single nodes in
     a classifier net as it is used by structured analysis of
     microarray data.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s_e_s:

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

_I_D is the GO identifier as character string

_s_u_p_N_o_d_e indicates whether the node is a supplementary node to avoid
     nodes which  have both, genes directly annotated and children in
     the stamNet.

_S_l_o_t_s:


     '_I_D': Object of class '"character"', holds the GO identifier as 
          character string

     '_c_a_t_e_g_o_r_y': Object of class '"character"', represents the GO 
          ontology the node belongs (MF: molecular function, BP:
          biological process, CC:  cellular component).

     '_r_e_p_l_a_c_e_d_P_a_r_e_n_t_s': Object of class '"character"', holds all GO 
          identifiers of nodes which have been removed, because the had
          only one child.

     '_s_u_p_N_o_d_e': Object of class '"logical"', indicates whether the
          nodes  has been added to avoid nodes which  have both
          directly annotated genes as well as  children in the
          classifier graph

_M_e_t_h_o_d_s:


     _g_e_t_G_O_c_h_i_l_d_r_e_n 'signature(x = "stamNode")': returns the identifiers
          of the direct children of node x in the Gene Ontology.

     _g_e_t_G_O_c_h_i_l_d_r_e_n 'signature(x = "character")': returns the
          identifiers of  the direct children of the node with
          identifier x in the Gene Ontology.

     _g_e_t_G_O_p_a_r_e_n_t_s 'signature(x = "stamNode")': returns the identifiers
          of the direct parents of node x in the Gene Ontology.

     _g_e_t_G_O_p_a_r_e_n_t_s 'signature(x = "character")': returns the identifiers
          of the direct parents of the node with identifier x in the
          Gene Ontology.

     _g_e_t_G_O_t_e_r_m 'signature(x = "stamNode")': returns the GO term
          represented by node x.

     _g_e_t_G_O_t_e_r_m 'signature(x = "character")': returns the GO term
          represented by the node with identifier x.

     _p_r_i_n_t 'signature(x = "stamNode")' print information on the node.

     _w_r_i_t_e_H_T_M_L 'signature(x = "stamNode")' generate HTML information on
          the  node.

_A_u_t_h_o_r(_s):

     Claudio Lottaz

_S_e_e _A_l_s_o:

     'stamLeaf-class', 'stamINode-class'

