parsePsimi25Interaction       package:RpsiXML       R Documentation

_P_a_r_s_i_n_g _P_S_I-_M_I _2._5 _X_M_L _d_o_c_u_m_e_n_t_s _i_n_t_o _i_n_t_e_r_a_c_t_i_o_n_s

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

     The PSI-MI 2.5 XML format is used widely by many repositories to
     record protein-protein interaction data as well as protein complex
     data. This functions parse such files into interactions or
     complexes.

     'parsePsimi25Interaction' is the parser for interaction data and
     'parsePsimi25Complex' is the parser for complex data.

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

     parsePsimi25Interaction(psimi25file, psimi25source, verbose=TRUE)
     parsePsimi25Complex(psimi25file, psimi25source, verbose=FALSE)

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

psimi25file: character, file name or URL of the XML document 

psimi25source: A supported data repository source, see also
          'psimi25Source-class' 

 verbose: logical, whether the parsing state should be displayed
          verbosely.

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

     'psimi25Interaction' returns a list of 'psimi25InteractionEntry'
     objects, each represents one 'entry' in the XML document
     'psimi25Complex' returns a 'psimi25ComplexEntry' objects,
     representing the complex data from one XML document.

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

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

_R_e_f_e_r_e_n_c_e_s:

_P_S_I-_M_I _X_M_L _v_2._5 _d_a_t_a _e_x_c_h_a_n_g_e _f_o_r_m_a_t <URL:
     http://www.psidev.info/index.php?q=node/60>

_B_i_o_G_R_I_D <URL: http://www.thebiogrid.com>

_D_I_P <URL: http://dip.doe-mbi.ucla.edu/>

_H_P_R_D <URL: http://www.hprd.org/>

_I_n_t_A_c_t <URL: http://www.ebi.ac.uk/intact>

_M_I_N_T <URL: http://mint.bio.uniroma2.it/mint>

_M_I_P_S/_C_O_R_U_M <URL: http://mips.gsf.de/>

_S_e_e _A_l_s_o:

     'psimi25Interaction-class', 'psimi25InteractionEntry-class',
     'psimi25Complex-class' 'psimi25ComplexEntry-class',

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

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

     gridxml <- file.path(xmlDir, "biogrid_200804_test.xml")
     gridSet <- parsePsimi25Interaction(gridxml, BIOGRID.PSIMI25)

     intactxml <- file.path(xmlDir, "intact_2008_test.xml")
     intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25, verbose=TRUE)

     # parse complex data
     intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
     intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)

