intactGraph-class          package:Rintact          R Documentation

_C_l_a_s_s "_i_n_t_a_c_t_G_r_a_p_h"

_D_e_s_c_r_i_p_t_i_o_n:

     A class representing the IntAct data as a graph. It is a 
     superclass of the graph class.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are usually created by 'intactXML2Graph'.

_S_l_o_t_s:


     '_i_n_t_e_r_a_c_t_o_r_s': matrix, Each row represents one interactor. IntAct
          IDs are used as row names. Each column represents one
          annotation.  Annotations include: UniProt ID, gene symbol,
          full name, locus name, ORF name, organism name, and NCBI
          taxonomy ID. Only those interactors which are  the nodes of
          the intactGraph is given.

_M_e_t_h_o_d_s:


     _s_h_o_w 'signature(object = "intactGraph")': a print method

     _t_r_a_n_s_l_a_t_e_I_n_t_a_c_t_I_D 'signature(object = "intactGraph")':  a method
          to translate IntAct codes to the various annotations.

     _t_r_a_n_s_l_a_t_e_N_o_d_e_I_D 'signature(object = "intactGraph")': a method that
          takes an intactGraph and translates each node ID from  the
          IntAct accension IDs to any other supported identifier.

_A_u_t_h_o_r(_s):

     T Chiang

_S_e_e _A_l_s_o:

     'intactXML2Graph'

