integrinMediatedCellAdhesion      package:graph      R Documentation

_K_E_G_G _I_n_t_e_g_r_i_n _M_e_d_i_a_t_e_d _C_e_l_l _A_d_h_e_s_i_o_n _g_r_a_p_h

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

     A graph representing the integrin-mediated cell adhesion 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(integrinMediatedCellAdhesion)

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

     The 'integrinMediatedCellAdhesion' data set contains three
     objects:

     The first is 'IMCAGraph', which is an object of class 'graph-NEL'
     and represents the hsa04510 graph from 'KEGG'.

     The second is 'IMCAAttrs', which is a data.frame with two columns,
     and a row for every node in 'IMCAGraph'.  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, 'IMCALocusLink' is a named list where the names
     correspond to the node names in 'IMCAGraph'.  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/hsa04510.html>

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

     data(integrinMediatedCellAdhesion)
     if (require("Rgraphviz") & interactive())
       plot(IMCAGraph)

