psimi25XML2Graph           package:RpsiXML           R Documentation

_C_o_n_v_e_r_t _a _v_e_c_t_o_r _o_f _P_S_I-_M_I _2._5 _X_M_L _f_i_l_e_s _i_n_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 function 'psimi25XML2Graph' take a vector of XML 2.5 files
     from te same data source and generates a graph object based on the
     type of the files.

_U_s_a_g_e:

     psimi25XML2Graph(psimi25files, psimi25source, type = "interaction",
     directed = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

psimi25files: Single file name or a vector of PSI-MI 2.5 XML file names
          or URLs. In case of splitted data the latter form is
          preferred. Different datasets or datasets from different
          sources should not be put into the same vector. 

psimi25source: Source of the PSI-MI 2.5 XML file, see
          'psimi25Source-class' 

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

directed: Logical, whehter the returned graph object should be directed
          or undirected 

     ...: Other parameters passed to 'parsePsimi25Interaction' 

_V_a_l_u_e:

     If type is "interaction",  then a resulting psimi25Graph object is
     genertated on the aggregation of the XML files. Otherwise if type
     is "complex,", a resulting psimi25HyperGraph object is generated
     on the aggregate of the XML files.

_A_u_t_h_o_r(_s):

     Jitao David Zhang, Tony Chiang

_S_e_e _A_l_s_o:

     'psimi25Source-class', 'psimi25Graph-class',
     'psimi25Hypergraph-class'

_E_x_a_m_p_l_e_s:

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

     intactxml <- file.path(xmlDir, "intact_2008_test.xml")
     intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25, type="interaction")

     intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
     intactComplexGraph <- psimi25XML2Graph(intactComplexxml, INTACT.PSIMI25, type="complex")

