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 sub-class of pubRepo that is implemented
     specifically to parse data from Gene Ontology. `readData' has been
     over wirtten 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 instatiate
     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 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'

_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: http://www.godatabase.org>

_S_e_e _A_l_s_o:

     `pubRepo-class'

_E_x_a_m_p_l_e_s:

     # Read a truncated version of GO.xml from Bioconductor
     go <- GO(srcUrl =
     "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml")
     goxml <- readData(go, xml = TRUE)