getGEOSAGE             package:SAGElyzer             R Documentation

_A_u_t_o_m_a_t_i_c_a_l_l_y _d_o_w_n_l_o_a_d_s _S_A_G_E _l_i_b_r_a_r_i_e_s _f_r_o_m _N_C_B_I

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

     Given an organism name (e.g. human) and a correct url,
     'getGEOSAGE' downloads SAGE libraries and stores them in a
     specified directory

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

     getGEOSAGE(organism = "human", targetDir = "", quiet = TRUE, url =
     "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
     getFileNames(organism, url)
     getSampleId(url)

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

organism: A character string for the name of the organism of interests

targetDir: A character string for the directory where the downloaded
          SAGE libraries will be stored

   quiet: A boolean indicating whether the status message from
          'download.file' will be supressed

     url: A character string for part of the url from which SAGE
          libraries will be downloaded

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

     'getGEOSAGE' downloads SAGE libraries from NCBI's GEO site and
     stores them in a specified directory. The url passed is the
     location where the cgi resides and will be appended the correct
     parameters that specifies the content and format of the data file
     to be downloaded.

     The system relies on GPL numbers that differ among organisms to
     find the correct platform sample ids for files belonging to a
     given organism. The platform sample ids will then be used to fetch
     the desired annotation files. 'getFileNames' gets the correct GPL
     number and 'getSampleId' gets the platform sample ids. 'parseSAGE'
     parses the downloaded file and stores the data to a specified
     place.

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

getFileNames: Returns a vector of GPL numbers

getSampleId: Returns a vector of platform sample ids

_W_A_R_N_I_N_G:

     ....

_N_o_t_e:

     The functions are part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide bioinformatics functionalities through
     R

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

     J. Zhang

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

     <URL: http://www.ncbi.nlm.nih.gov/geo/query/>

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

     'mergeSAGE'

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

     # Since downloading and parsing SAGE libraries are time consuming, the
     # example code is inactivated.
     ## Not run: 
     getGEOSAGE(organism = "human", targetDir = "", quiet = TRUE, url =
     "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
     ## End(Not run)  

