resourcerer2BioC         package:Resourcerer         R Documentation

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_R_e_s_o_u_r_c_e_r_e_r _a_n_d _t_h_e_n _c_r_e_a_t_e_s _a _b_i_o_C _a_n_n_o_t_a_t_i_o_n _d_a_t_a _p_a_c_k_a_g_e

_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 create a bioC
     annotation data package for the probes contained in the
     Resourcerer annotation file.

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

      
     resourcerer2BioC(which, organism = c("human", "mouse", "rat"),
         destDir = file.path(.path.package("Resourcerer"), "temp"),
         pkgName, pkgPath, baseMapType = c("gbNRef", "gb", "ug", "ll"),
         version = "1.1.0", baseUrl =
         "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", check =
         FALSE, author = list(authors = "Anonymous", maintainer
          = "Anonymous <anonymous@email.com>"), exten = "zip")

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

   which: 'which' a character string indicating which Resourcerer
          annotation file to be read in

 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

baseMapType: 'baseMapType' a character string that is either "gb","ug",
          or "ll" to indicate whether the probe ids in baseName are
          mapped to GenBack accession numbers, UniGene ids, or
          LocusLink ids

 pkgName: 'pkgName' a character string for the name of the data package
          to be built (e. g. hgu95a, rgu34a)

 pkgPath: 'pkgPath' a character string for the full path of an existing
          directory where the built backage will be stored

organism: 'organism' a character string for the name of the organism of
          concern (now can only be "human", "mouse", or "rat")

 version: 'version' a character string for the version number

  author: 'author' a list of character strings with an author element
          for the name of the author and maintainer element for the
          email address of the author

   check: 'check' a boolean incicating whether to check the mappings
          between probe ids and LocusLink ids obtained from Resourcer
          and bioC AnnBuilder when baseMapType is 'll'

   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 resourcerer2BioC returns invisible() if successfully
     executed.

_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:

     'getResourcerer'

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

       #############################################################
       ## The example takes a loooong time (about an hour) to run ##
       #############################################################
       if(interactive()){
         resourcerer2BioC("Agilent_Human1_cDNA.zip",  baseMapType = "gbNRef")
         unlink(file.path(.path.package("Resourcerer"), "temp",
                "AgilentHuman1cDNA"), TRUE)
       }    

