GOPkgBuilder           package:AnnBuilder           R Documentation

_F_u_n_c_t_i_o_n_s _t_o _b_u_i_l_d _a _d_a_t_a _p_a_c_k_a_g_e _u_s_i_n_g _G_O _d_a_t_a

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

     These functions creates data, documentation, and other supporting
     files that consist an annotation data package using data from GO.

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

     GOPkgBuilder(pkgName, pkgPath, filename, version, author, lazyLoad=TRUE)
     writeDocs(baseName, pkgName, pkgPath, version, author, repList, pattern,
     isFile = TRUE) 
     copyTemplates(repList, pattern, pkgName, pkgPath, replaceBy = NULL)
     getRepList(what, srcObjs)

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

 pkgName: 'pkgName' a character string for the name of the data package
          to be built

 pkgPath: Describe 'pkgPath' a character string for the path to which
          the data package to be built will be stored

filename: Name of the GO file to parse.  This file should be from the
          GO website in OBO XML format.

 version: 'version' a character string for the version number of the
          data package

  author: 'author' a named vector of character string with a name
          element for the name of the author and address element for
          the email address of the author

 repList: 'repList' a list with LLSOURCE, GOSOURCE, LLBUILT, GOBUILT,
          and DATE elements containing source url or built date
          information that will be used to replace corresponding texts
          in man page templates stored in the templates subdirectory

 pattern: 'pattern' a character string that will be used as a pattern
          to copy man page templates files in the "templates"
          subdirectory to the "man" subdirectory of a newly created
          data package using the function copySubstitute of Biobase

replaceBy: 'replaceBy' a character string specifying the text used to
          replace the pattern contained by the name of a template man
          page files when writing to a newly created data package

    what: 'what' a character string for the name of the data package to
          be created for which a replacement list will be generated

baseName: 'baseName' a character string for the name of the base file
          based on which a data package was built. "" if there is none

 srcObjs: 'srcObjs' a list containing source data objects that are sub
          classes of pubRepo

  isFile: 'isFile' a boolean indicating whether 'baseName' is a file or
          an R object

lazyLoad: 'lazyLoad' a boolean indicating whether a lazy load database
          will be created

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

     This package relies on the xml data file from <URL:
     http://www.godatabase.org/dev/database/archive/2003-04-01/go_200304-termdb.xml.gz>
     to obtain the data. The url changes when data are updated. The
     system has built in code to figure out where the latest data are
     and use that data to build the data package.

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

     This function does not return any value

_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://www.godatabase.org>

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

     'ABPkgBuilder', 'KEGGPkgBuilder'

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

     if(interactive()){
     GOPkgBuilder(pkgName = "GO", pkgPath = tempdir(), version = "1.2.1",
     goUrl = "http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml",
     author = c(author = "who", maintainer = "who@email.com"))
     list.files(file.path(tempdir(), "GO"))
     unlink(file.path(tempdir(), "GO"), TRUE)
     }

