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. 'psimi25XML2Graph' is a wrapper for
     'interactionEntry2graph' and 'complexEntry2graph', which transform
     interactionEntry list and complexEntry list into graphs
     respectively.

_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")

