separateXMLDataByExpt        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 _b_a_s_e_d _o_n _p_u_b_m_e_d_I_D

_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:

     separateXMLDataByExpt(xmlFiles, psimi25source, type = "direct", directed = TRUE, abstract = FALSE,...)

_A_r_g_u_m_e_n_t_s:

xmlFiles: Single file name or a vector of PSI-MI 2.5 XML file names or
          URLs.

    type: A character. Currently the user can specify to cull either
          "direct" interactions or "indirect" interactions.

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

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

abstract: Logical; if TRUE, the abstract information will be appended
          to the graph object.

     ...: Other parameters passed to 'parsePsimi25Interaction', for
          example 'verbose=TRUE'

_V_a_l_u_e:

     A list of 'psimi25Graph-class' are generated indexed by the
     pubmedID of each bait-prey interaction. WARNING - the abstract
     information is obtained using the  pubmed and buildPubMedAbst
     functions from the  annotate package which warns the user that
     NCBI may block access to their site. The default is to not obtain
     the abstract for this reason.

_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 <- separateXMLDataByExpt(intactxml, INTACT.PSIMI25)

