parseKGMLexpandMaps        package:KEGGgraph        R Documentation

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_m_a_p_s _i_n_t_o _o_n_e _g_r_a_p_h _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     The function does several tasks implemented in the KEGGgraph
     package in sequence to make expanding maps easier.

_U_s_a_g_e:

     parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,...)

_A_r_g_u_m_e_n_t_s:

    file: A KGML file 

downloadmethod: passed to 'download.file' function as 'method', see its
          documentation for more details 

genesOnly: logical, should only the genes nodes remain in the returned
          graph object? 

localdir: character string, if specified, the function tries to read
          files with the same base name from a local directory, useful
          when there are file copies on the client.

     ...: Other parameters passed to  'download.file' 

_D_e_t_a_i_l_s:

     In KEGG pathways there're usually pathways
     contained('cross-linked') in other pathways, for example see <URL:
     http://www.genome.jp/kegg/pathway/hsa/hsa04115.html>, where p53
     signalling pathway contains other two pathways 'apoptosis' and
     'cell cycle'. This function parses these pathways (refered as
     'maps' in KGML manual), download their KGML files from KEGG FTP
     website, parse them individually, and merge all the children
     pathway graphs with the parental pathway into one graph object.
     The graph is returned as the function value.

     Since different graphs does not have unique node identifiers
     unless the genes are expanded, so by using this function user has
     to expand the genes. Another disadvantage is that so far due to
     the implementation, the KEGGnodeData and KEGGedgeData is lost
     during the merging. This however will probably be changed in the
     future version.

_V_a_l_u_e:

     A directed graph object

_A_u_t_h_o_r(_s):

     Jitao David Zhang <URL: j.zhang@dkfz.de>

_R_e_f_e_r_e_n_c_e_s:

     KGML Document manual <URL: http://www.genome.jp/kegg/docs/xml/>

_S_e_e _A_l_s_o:

     for most users it is enough to use 'parseKGML2Graph'

