KEGGpathway2Graph         package:KEGGgraph         R Documentation

_P_a_r_s_e_s _K_E_G_G_p_a_t_h_w_a_y _t_o _g_r_a_p_h

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

     The function parses an object of 'KEGGPathway-class' into graph.

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

     KEGGpathway2Graph(pathway, genesOnly = TRUE, expandGenes = TRUE)

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

 pathway: An instance of 'KEGGPathway-class' 

genesOnly: logical, should only the genes are maintained and other
          types of nodes (compounds, etc) neglected? TRUE by default

expandGenes: logical, should homologue proteins expanded? TRUE by
          default 

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

     When 'expandGenes=TRUE', the nodes have unique names of KEGGID (in
     the form of 'org:xxxx', for example 'hsa:1432'), otherwise an
     auto-increment index given by KEGG is used as node names. In the
     latter case, the node names are duplicated and graphs cannot be
     simply merged before the nodes are unique.

     KEGG node and edge data is stored in 'nodeData' and 'edgeData'
     slots respectively, which can be extracted by 'getKEGGnodeData'
     and 'getKEGGedgeData'.

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

     A directed graph.

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

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

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

     'parseKGML2Graph'

_E_x_a_m_p_l_e_s:

     sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
     kegg.pathway <- parseKGML(sfile)
     gR.compact<- KEGGpathway2Graph(kegg.pathway,expandGenes=FALSE)

