getKEGGdata         package:domainsignatures         R Documentation

_F_e_t_c_h _K_E_G_G _a_n_n_o_t_a_t_i_o_n_s _a_n_d _I_n_t_e_r_P_r_o _d_o_m_a_i_n_s

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

     Get all available KEGG annotations and InterPro domains for a set
     of entrezgene identifiers from the 'KEGG' annotation package and
     from the ensembl 'biomaRt'.

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

     getKEGGdata(universe, pathways)

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

universe: Character vector of entrezgene identifiers. This is the
          global universe of genes to test against.

pathways: Optional character vector of KEGG pathway identifiers. This
          can be used in order to test for over-representation of only
          a subset of all the available KEGG pathways. 

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

     This function is a wrapper around the 'KEGG' annotation package
     and a customized query of the ensembl 'biomaRt' database. For the
     gene identifiers in 'universe' and all KEGG pathways it will fetch
     the necessary information and create an object of class
     'ipDataSource' which can later be used as input to 'gseDomain'

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

     An object of class 'ipDataSource'.

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

     Florian Hahne

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

     'gseDomain'

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

     getKEGGdata()

