availableXrefs            package:RpsiXML            R Documentation

_G_e_t _c_r_o_s_s _r_e_f_e_r_e_n_c_e(_s) _o_f _i_n_t_e_r_a_c_t_o_r_s _f_r_o_m _P_S_I-_M_I _2._5 _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     PSI-MI 2.5 data exchange format encourages data providers to
     encode cross referenes of the interactors into the file, which
     prove valuable for annotating the data. These functions help
     finding out the available cross references of interactors.

_U_s_a_g_e:

     availableXrefs(x,...)
     xref(x,...)

_A_r_g_u_m_e_n_t_s:

       x: for 'availableXrefs', 'x' can either be an object of
          'psimi25Interactor-class',  'link{psimi25InteractionEntry}'
          or a list of 'psimi25Interactor-class' objects.

          for 'xref', 'x' should be an object of
          'psimi25Interactor-class' 

     ...: intersect, logical option. If set to 'TRUE' then only the
          cross references available for every interactor are returned
          (intersected), otherwise all the cross references are unioned
          and returned. See the examples

_D_e_t_a_i_l_s:

     If 'psimi25InteractionEntry' is provided as the parameter of
     'availableXrefs', an option named "intersect" can be set to
     extract only those cross references intersected among all the
     interactors, namely the ones assigned in every interactor. Please
     see the examples.

_V_a_l_u_e:

   xref : Returns a matrix with two columns: 'db' (external database
          name) and 'id' (external database index) 

availableXrefs : A vector of characters, the names of external
          databases referenced in the file

_A_u_t_h_o_r(_s):

     Jitao David Zhang

_E_x_a_m_p_l_e_s:

     xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")

     hprdxml <- file.path(xmlDir, "hprd_200709_test.xml")
     hprdSet <- parsePsimi25Interaction(hprdxml, HPRD.PSIMI25)
     hprdInteractors <- interactors(hprdSet)

     availableXrefs(hprdSet)
     xref(hprdInteractors[[1]])
     availableXrefs(hprdInteractors[[1]])

