GEO-class             package:AnnBuilder             R Documentation

_C_l_a_s_s "_G_E_O" _r_e_p_r_e_s_e_n_t_s _a _G_E_O _o_b_j_e_c_t _t_h_a_t _r_e_a_d_s/_d_o_w_n_l_o_a_d_s _d_a_t_a
_f_r_o_m _t_h_e _G_E_O _w_e_b _s_i_t_e

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

     The GEO web site contains data files represented by GEO accession
     numbers. Class GEO reads/downloads data files from the site if
     correct url and GEO accession numbers are provided

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

_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 a CGI script that handles
          data requests, which is: <URL:
          http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?> at the time
          of writing 

_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 = "GEO")': reads data from GEO and then
          parses the data to a matrix

_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:

     Programming with data

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

     'queryGEO','pubRepo-class'

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

     ## Not run: 
     geo <- GEO("http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
     # The GEOAccNum may be invalid due to changes at GEO site
     data <- readData(geo, GEOAccNum = "GPL16" )
     ## End(Not run)

