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, type="indirect")

