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. In
     general, the entry of this function should be that data from one
     experiment  (this data might be divided into several XML files).
     If the XML file contains data that should not be combined into one
     single graph,  this function should not be called; the function 
     'separateXMLDataByExpt' should be used instead.

_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:

     Rintact: enabling computational analysis of molecular interaction
     data from the IntAct repository - Tony Chiang; Nianhua Li; Sandra
     Orchard; Samuel  Kerrien; Henning Hermjakob; Robert Gentleman;
     Wolfgang Huber Bioinformatics 2007; doi:
     10.1093/bioinformatics/btm518.

_S_e_e _A_l_s_o:

     'interactionEntry-class', 'complexEntry-class',        
     'separateXMLDataByExpt'

