KEGG-class            package:AnnBuilder            R Documentation

_C_l_a_s_s "_K_E_G_G" _a _s_u_b-_c_l_a_s_s _o_f _p_u_b_R_e_p_o _t_o _g_e_t/_p_r_o_c_e_s_s _p_a_t_h_w_a_y _a_n_d
_e_n_z_y_m_e _i_n_f_o_r_m_a_t_i_o_n

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

     This class is a sub-class of pubRepo with source specific
     functions to get/process data from KEGG {<URL:
     ftp://ftp.genome.ad.jp/pub/kegg/pathways>} to obtain pathway and
     emzyme information for genes

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("KEGG", ...)'. A
     constructor (KEGG) is available and should be used to instantiate
     objects of this class

_S_l_o_t_s:

     '_o_r_g_a_n_i_s_m': Object of class '"character", from class "UG"' a
          character string for the organism of concern

     '_s_r_c_U_r_l': Object of class '"character", from class "UG"' a
          character string for the url where source data are stored
          (<URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways>) at the time
          of coding

     '_p_a_r_s_e_r': Object of class '"character", from class "UG"' not in
          use

     '_b_a_s_e_F_i_l_e': Object of class '"character", from class "UG"' not in
          use

_E_x_t_e_n_d_s:

     Class '"UG"', directly. Class '"pubRepo"', by class "UG".

_M_e_t_h_o_d_s:

     _f_i_n_d_I_D_N_P_a_t_h 'signature(object = "KEGG")': Finds the mappings
          between KEGG ids and pathway names

     _m_a_p_L_L_2_E_C_N_P_N_a_m_e 'signature(object = "KEGG")': Maps LocusLink ids to
          enzyme ids and pathway names

_N_o_t_e:

     This class is part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua Zhang

_R_e_f_e_r_e_n_c_e_s:

     <URL: www.genome.ad.jp/kegg/>

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

     'pubRepo-class', 'UG-class'

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

     ## Not run: 
     # The url (\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}) may change but
     # was correct at the time of coding
     url <-  getSrcUrl("KEGG")
     kegg <- KEGG(srcUrl = url, organism = "human")
     pathNEnzyme <- mapLL2ECNPName(kegg)
     ## End(Not run)

