GO-class             package:AnnBuilder             R Documentation

_C_l_a_s_s "_G_O" _a _c_l_a_s_s _t_o _h_a_n_d_l_e _d_a_t_a _f_r_o_m _G_e_n_e _O_n_t_o_l_o_g_y

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

     This class is a sub-class of pubRepo that is implemented
     specifically to parse data from Gene Ontology. 'readData' has been
     over written to process Gene Ontology data

_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("GO", ...)'. A
     constructor ('GO' is available and should be used to instantiate
     objects of GO).

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

     '_s_r_c_U_r_l': Object of class '"character", from class "pubRepo"' a
          character string for the url of the source data from Gene
          Ontology

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

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

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

     Class '"pubRepo"', directly.

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

     _r_e_a_d_D_a_t_a 'signature(object = "GO")': Downloads/processes
          go_xxx-termdb from Gene Ontology, where xxx is a date. If
          argument xml is set to be TRUE, the data file will be parsed
          and a matrix with three columns will be returned. The first
          column is for GO ids, second for the GO ids of its direct
          parents, and third for the ontology term defined by Gene
          Ontology. Otherwise, the data (not in xml form) will be read
          in using 'readLines'

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

     Jianhua Zhang

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

     <URL: http://www.godatabase.org>

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

     'pubRepo-class'

