intactXML2Graph           package:Rintact           R Documentation

_A _f_u_n_c_t_i_o_n _t_h_a_t _t_a_k_e_s _a _v_e_c_t_o_r _o_f _I_n_t_A_c_t _X_M_L _f_i_l_e _n_a_m_e_s
_a_n_d _c_o_n_v_e_r_t_s _t_h_e_m _t_o _g_r_a_p_h _o_b_j_e_c_t_s.

_D_e_s_c_r_i_p_t_i_o_n:

     The 'intactXML2Graph' takes in a vector of related XML files and
     generates a graph object based on the type of XML file.

_U_s_a_g_e:

     intactXML2Graph(intactFiles, type="interaction", directed=TRUE)

_A_r_g_u_m_e_n_t_s:

intactFiles: A vector of IntAct XML file names. If the data  of a
          single experiment has been split into multiple XML files 
          (e.g. Ewing et al 2007), then each entry of the vector should
          contain one of these XML files. NB - different datasets
          should not be  put into the same vector.

    type: A character string which is either "interaction" if the XML
          file contains experimental physical data or "complex" if the 
          XML file contains curated protein complex membership data.

directed: A logical. User defined parameter so that the return value
          with either be a directed or undirected graph object.

_V_a_l_u_e:

     If type = "interaction," then a resulting intactGraph object is
     genertated on the aggregate of the XML files. If type = "complex,"
     then a resulting intactHyperGraph object is generated on the
     aggregate of the XML files.

_A_u_t_h_o_r(_s):

     T Chiang

_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

