psimi25InteractionEntry-class    package:RpsiXML    R Documentation

_C_l_a_s_s "_p_s_i_m_i_2_5_I_n_t_e_r_a_c_t_i_o_n_E_n_t_r_y"

_D_e_s_c_r_i_p_t_i_o_n:

     A class representing interaction data parsed from PSI-MI 2.5 XML
     files

_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
     'parsePsimi25Interaction'

_S_l_o_t_s:


     '_o_r_g_a_n_i_s_m_N_a_m_e': Object of class '"character"', the unique organism
          name(s) of the interactors 

     '_t_a_x_I_d': Object of class '"character"', the unique NCBI taxonomy
          ID(s) of the interactors 

     '_r_e_l_e_a_s_e_D_a_t_e': Object of class '"character"', character, release
          date of the data entry,  recorded in the 'entry' element of
          the XML file

     '_i_n_t_e_r_a_c_t_o_r_s': Object of class '"matrix"', interactor information
          in a matrix, Each row represents one interactor. Source IDs
          are used as row names. Each column represents one annotation.
           Annotations include: UniProt ID, short label, organism name,
          and NCBI taxonomy ID 

     '_i_n_t_e_r_a_c_t_i_o_n_s': Object of class '"list"', list, a list of
          'psimi25Interaction-class' objects,  each represents one
          interaction. 

_M_e_t_h_o_d_s:


     _i_n_t_e_r_a_c_t_i_o_n_s 'signature(x = "psimi25InteractionEntry")': return a
          list of 'psimi25Intearaction' objects, each representing one
          interaction

     _i_n_t_e_r_a_c_t_o_r_s 'signature(x = "psimi25InteractionEntry")': a method
          to find  all the interactors within the
          psimi25InteractionEntry and print them 

     _o_r_g_a_n_i_s_m_N_a_m_e 'signature(x = "psimi25InteractionEntry")': returns
          organism names of the interactors 

     _r_e_l_e_a_s_e_D_a_t_e 'signature(x = "psimi25InteractionEntry")': returns
          the release date, serving as a proxy for versioning 

     _s_h_o_w 'signature(object = "psimi25InteractionEntry")': a print
          method

     _t_a_x_I_d 'signature(x = "psimi25InteractionEntry")': returns NCBI
          taxonomy ID 

_A_u_t_h_o_r(_s):

     Tony Chiang <tchiang@ebi.ac.uk> , Jitao David Zhang
     <j.zhang@dkfz.de>

_S_e_e _A_l_s_o:

     'parsePsimi25Interaction', 'S4classpsimi25Interaction-class'

_E_x_a_m_p_l_e_s:

     showClass("psimi25InteractionEntry")

