translateKEGGID2GeneID       package:KEGGgraph       R Documentation

_T_r_a_n_s_l_a_t_e _b_e_t_w_e_e_n _K_E_G_G_I_D _a_n_d _E_n_t_r_e_z _G_e_n_e _I_D

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

     'translateKEGGID2GeneID' translates KEGGID to NCBI Entrez Gene ID,
     and 'translateGeneID2KEGGID' translates Entrez Gene ID back to
     KEGGID.

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

     translateKEGGID2GeneID(x, organism="hsa")
     translateGeneID2KEGGID(x, organism="hsa")

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

       x: KEGGID, e.g. 'hsa:1432', or Entrez Gene ID, e.g. '1432' 

organism: Three alphabet code for organisms. The mapping between the
          orgniams and codes can be found at <URL:
          http://www.genome.jp/kegg/kegg3.html>

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

     The KEGGID are unique identifiers used by KEGG PATHWAY to identify
     gene products. After parsing the KEGG pathway into graph, the
     graph use KEGGID as its nodes' names.

     'translateKEGGID2GeneID' converts KEGGIDs into entrez GeneID,
     which can be translated to other types of identifiers, for example
     with biomaRt package or organism-specific annotation packages. See
     vignette for examples.

     'translateKEGG2GeneID' is maintained for back-compatibility and
     wrapps 'translateKEGGID2GeneID'.

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

     Entrez GeneID of the given KEGG ID(s)

_N_o_t_e:

     This function works so far only with human KEGGIDs, since for them
     the Entrez GeneID can be derived easily with removing the organism
     prefix.

     The complete functional function will be implemented in the later
     release of the package.

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

     Jitao David Zhang

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

     egNodes <- c("hsa:1432", "hsa:11072")
     translateKEGGID2GeneID(egNodes)
     translateGeneID2KEGGID("1432")

