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]])

