keggDF2graph            package:keggorth            R Documentation

_c_r_e_a_t_e _a _g_r_a_p_h _f_r_o_m _a _s_p_e_c_i_f_i_c _d_a_t_a _f_r_a_m_e _f_o_r_m_a_t
_f_o_r _K_E_G_G _o_r_t_h_o_l_o_g_y

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

     create a graph from a specific data frame format for KEGG
     orthology

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

     keggDF2graph(df, root="KO.June07root")
     data(KOgraph)

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

      df: the data frame

    root: a name for root node

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

     the obvious directed graph structure from root to leaf nodes
     (pathway names) is instantiated for the orthology, nodeData
     attribute tag is loaded with the numerical tag for the term in
     KEGG, and nodeData attribute depth is loaded with depth from root

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

     a 'graphNEL-class' instance

_N_o_t_e:

     This is only a support function.  The graph is serialized in the
     package data directory.

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

     Vince Carey <stvjc@channing.harvard.edu>

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

     data(keggOrthDF)
     keggOrthDF[1:5,]
     data(KOgraph)
     nodes(KOgraph)[1:4]
     nodeData(KOgraph,,"tag")[1:5]
     nodeData(KOgraph,,"depth")[1:5]

