getResourcerer          package:Resourcerer          R Documentation

_A _f_u_n_c_t_i_o_n _t_h_a_t _d_o_w_n_l_o_a_d_s _a_n _a_n_n_o_t_a_t_i_o_n _f_i_l_e _f_r_o_m _T_I_G_R
_R_e_s_o_u_r_c_e_r_e_r _a_n_d _t_h_e_n _r_e_a_d _t_h_e _d_o_w_n_l_o_a_d_e_d _f_i_l_e _i_n _a_s _a _m_a_t_r_i_x

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

     TIGR Resourcerer maintains various annotation files for Affymetrix
     or cDNA chips. This function allows users to read an annotation
     file into R as a matrix.

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

     getResourcerer(which, organism, destDir =
     file.path(.path.package("Resourcerer"), "temp"), baseUrl =
     "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip")  

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

   which: 'which' a character string indicating which annotation file
          to be read in. The annotation files are stored in
          subdirectories for various organisms under 'baseUrl' (see
          below)

organism: 'organism' a character string for the name of the organism of
          interests

 destDir: 'destDir' a character string for the path of a directory
          where the downloaded file will be stored. If missing, the
          temp directory will be the default

 baseUrl: 'baseUrl' a character string for the url of Resourcerer ftp
          site where directories containing annotation files for human,
          rat, mouse ... are stored

   clean: 'clean' a boolean indicating whether the file downloaded from
          Resourcerer will be removed after the data contained have
          been read in

   exten: 'exten' a character string for the extension (e. g. zip) of
          the source data file to be processed

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

     'baseUrl' is the root directory of TIGR ftp site for Resourcerer
     that contains subdirectories holding data for different organism.

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

     Function getResourcerer returns a matrix derived from the source
     data. Column names of the returned matrix are taken directly from
     the source file provided by Resourcerer. Users are advised to
     visit the Resourcerer web site for more information about the
     source data files.

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

     Jianhua Zhang

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

     <URL: http://pga.tigr.org/tigr-scripts/magic/r1.pl>

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

     'resourcerer2BioC'

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

       resourcerer <- getResourcerer("Agilent_Human1_cDNA.zip", organism = "human",
            destDir = file.path(.path.package("Resourcerer"), "temp"),
            baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer",
            clean = TRUE, exten = "zip")
       resourcerer[1:3,]
       
       

