apoptosisGraph             package:graph             R Documentation

_K_E_G_G _a_p_o_p_t_o_s_i_s _p_a_t_h_w_a_y _g_r_a_p_h

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

     A graph representing the apoptosis pathway from KEGG, as well as a
     data.frame of attributes for use in plotting the graph with
     'Rgraphviz' and a list to compare the nodes with their respective
     LocusLink IDs.

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

     data(apopGraph)

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

     The 'apopGraph' data set contains three objects:

     The first is 'apopGraph', which is an object of class 'graph-NEL'
     and represents the hsa04210 graph from 'KEGG'.

     The second is 'apopAttrs', which is a data.frame with two columns,
     and a row for every node in 'apopGraph'.  The first column lists
     what color the node is represented with on the 'KEGG' site.  The
     second column lists the type of the node - either 'genesym' or
     'text'.  Most nodes are of type 'genesym' as they represent genes,
     but some of the nodes in the 'KEGG' graph were not genes and thus
     those nodes are of type 'text'.

     The third, 'apopLocusLink' is a named list where the names
     correspond to the node names in 'apopGraph'.  The values of the
     list are the LocusLink IDs that correspond to that node in the
     KEGG graph.

_S_o_u_r_c_e:

     <URL: http://www.genome.ad.jp/kegg/pathway/hsa/hsa04210.html>

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

     data(apopGraph)
     if (require("Rgraphviz") & interactive())
       plot(apopGraph)

