psi25interaction           package:Rintact           R Documentation

_p_a_r_s_e_r _f_o_r _P_S_I-_M_I _2._5 _X_M_L _d_o_c_u_m_e_n_t_s _f_r_o_m _E_B_I _i_n_t_a_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     The PSI-MI 2.5 XML format is used by EBI IntAct database to record
     protein-protein interaction data and protein complex data. 
     'psi25interaction' is the parser for interaction data and
     'psi25complex' is the parser for complex data.

_U_s_a_g_e:

     psi25interaction(intactFile)
     psi25complex(intactFile)

_A_r_g_u_m_e_n_t_s:

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

_V_a_l_u_e:

     'psi25interaction' returns a list of 'interactionEntry'  objects,
     each represents one 'entry' in the XML document. 'psi25complex'
     returns an 'complexEntry' object, which represents the data from
     one XML document.

_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:

     'interactionEntry-class', 'complexEntry-class'

_E_x_a_m_p_l_e_s:

     # parse complex data
     fn <- system.file("PSI25XML/complexSample.xml", package="Rintact")
     complexData <- psi25complex(fn)
     complexData

     # parse interaction data
     fn <- system.file("PSI25XML/interactionSample.xml", package="Rintact")
     interactionData <- psi25interaction(fn)
     interactionData

