writeManPage           package:PAnnBuilder           R Documentation

_W_r_i_t_e _H_e_l_p _D_o_c_u_m_e_n_t_s

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

     Given the R environment in the data directory, these functions
     write help documents based on templates and stored them in the man
     directory.

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

      
     getRepList(organism="", type, srcUrls="", built="", pkgName)
     copyTemplates(repList, pattern, pkgName, pkgPath, replaceBy = NULL)
     copyTemplates_DB(repList, pkgName, pkgPath)
     writeDescription(pkgName, pkgPath, version, author, 
                      dataSrc = "public data repositories", 
                      license = "The Artistic License, Version 2.0")  
     writeDescription_DB(pkgName, pkgPath, version, author, organism,
                         dataSrc = "public data repositories",
                         license = "The Artistic License, Version 2.0") 
         
     writeManAnno(pkgName, pkgPath, version, author, repList, pattern) 
     writeManAnno_DB(pkgName, pkgPath, version, author, repList)
     writeManSQ(pkgName, pkgPath, version, author, repList)
     writeManMerge(pkgName, pkgPath, version, author, repList, pattern) 

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

organism: a character string for the name of the organism of concern.
          (eg: "Homo sapiens")

    type: a character string for the concerned database. Possible
          values of  type are : "sp", "trembl", "ipi", "refseq",
          "geneint", "intact", "mppi",  "3DID", "DOMINE", "BaCelLo",
          "DBSubLoc", "SCOP", "HomoloGene", "InParanoid", 
          "PeptideAtlas", "SysPTM", "SysBodyFluid", "GOA", "GO",
          "KEGGNAME", "PFAMNAME",  "INTERPRONAME", "TAXNAME", "dName",
          "cross", "pSeq". 

 srcUrls: a character string or a string vector for the urls of
          database.

   built: a character string for the version/release information of
          database.

 repList: a named list which will replace the symbols in template file.

 pattern: a character string of the prefix of template *.Rd file 

replaceBy: a character string for the prefix of new *.Rd file.  If
          replaceBy=NULL, pattern will be replaed by pkgName. Otherwise
           pattern will be replaed by replaceBy 

 dataSrc: a character string describing the data source

 license: a character string describing the license of R package.  It
          will appear in the description file.

 pkgName: the name of the data package to be built. (e.g. "hsaSP") 

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

 version: a character string for the version number.

  author: a list with named elements "authors" containing a character
          vector of author names and "maintainer" containing the
          complete character string for the maintainer field, for
          example, "Jane Doe <jdoe@doe.com>".

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

     Write help document files for the package. 'getRepList' return a
     list which will replace the symbols in  template file.

     If the name of "*.rda" file in the "data" subdirectory matchs the
     pattern,  'copyTemplates' will produce a "*.rd" file in the "man" 
     subdirectory. Related template files in the "inst/templates"
     subdirectory  are needed for this function. 

     Parameter "names" gives the name of the data objects;
     'copyTemplates_DB'  will produces relative "*.rd" files in the
     "man" subdirectory. Related template  files in the
     "inst/templates" subdirectory are needed for this function. 

     'writeDescription' write descrption file for the environment-based
      annotation package.

     'writeDescription_DB' write descrption file for the SQLite-based  
     annotation package.    

     'writeManAnno' write help document files for the environment-based
      annotation package. 'writeManAnno_DB' write help document files
     for the SQLite-based  annotation package.

     'writeManSQ' write help document files for the sequence data 
     package.

     'writeManMerge'  write help document files for the merged package.

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

     Hong Li

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

     Zhang, J., Carey, V., Gentleman, R. (2003) An extensible
     application for  assembling annotation for genomic
     data.Bioinformatics 19(1), 155-156.

