interactionEntry-class        package:Rintact        R Documentation

_C_l_a_s_s "_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 the interaction data extracted from an IntAct
     data file in PSI-MI 2.5 format.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are usually created by 'psi25interaction'.

_S_l_o_t_s:


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

     '_o_r_g_a_n_i_s_m_N_a_m_e': character, the unique organism name(s) of the
          interactors.

     '_t_a_x_I_d': character, the unique NCBI taxonomy ID(s) of the
          interactors.

     '_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.

     '_i_n_t_e_r_a_c_t_i_o_n_e_s': list, a list of 'intactInteraction' objects, 
          each represents one interaction. 

_M_e_t_h_o_d_s:


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

     _b_a_i_t 'signature(object = "interactionEntry")': a method to find
          all the baits within the interactionEntry and print them

     _p_r_e_y 'signature(object = "interactionEntry")': a method to find
          all the  prey within the interactionEntry and print them

     _i_n_t_e_r_a_c_t_i_o_n_s 'signature(object = "interactionEntry")': a method to
          find all the interactions within the interactionEntry and
          print them

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

     _o_r_g_a_n_i_s_m_N_a_m_e 'signature(object = "interactionEntry")': a method to
          print all the unique organism names that are of the
          interactors 

     _t_a_x_I_d 'signature(object = "interactionEntry")': a method to print
          each taxonomy id for each organism

     _r_e_l_e_a_s_e_D_a_t_e 'signature(object = "interactionEntry")': a method to
          print  the updated release date of the PSI-MI 2.5 XML file;
          it serves as a proxy for versioning.

_A_u_t_h_o_r(_s):

     Nianhua Li

_R_e_f_e_r_e_n_c_e_s:

     The IntAct Database: <URL:
     http://www.ebi.ac.uk/intact/site/contents/downloads.jsf>.

_S_e_e _A_l_s_o:

     'intactInteraction-class', 'psi25interaction'

