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, srcUrls = getSrcUrl("all", switch(organism,
                    human = "Homo sapiens", mouse = "Mus musculus",
                                      rat = "Rattus norvegicus")),
                    otherSrc = NULL, baseMapType = c("gb", "ug", "ll"),
                    version = "1.1.0", makeXML = TRUE, fromWeb = TRUE,
                    baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/Resourcerer",
                    check = FALSE, author = list(author = "Anonymous",
                                   maintainer = "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

 srcUrls: 'srcUrls' a vector of names character strings for the urls
          where source data files are retained. Valid sources are
          LocusLink, UniGene, Golden Path, Gene Ontology, and KEGG. The
          names for the character strings should be LL, UG, GP, GO, and
          KEGG, respectively. LL and UG are required

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

otherSrc: 'otherSrc' a vector of named character strings for the names
          of files that contain mappings between probe ids of baseName
          and LocusLink ids that will be used to obtain the unified
          mappings between probe ids of baseName and LocusLink ids
          based on all the sources. The strings should not contain any
          number and the files have the same structure as baseName

 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

 makeXML: 'makeXML' a boolean to indicate whether an XML version will
          also be generated

  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

 fromWeb: 'fromWeb' a boolean indicating whether source files used to
          build a data package will be obtained on line

   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.

_N_o_t_e:

     This function 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://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")
         unlink(file.path(.path.package("Resourcerer"), "temp",
                "AgilentHuman1cDNA"), TRUE)
       }    

