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)

