cleanSrcObjs           package:AnnBuilder           R Documentation

_S_u_p_p_o_r_t_i_n_g _f_u_n_c_t_i_o_n _t_h_a_t _m_a_y _n_o _o_f _a_n_y _o_t_h_e_r _u_s_e_s_e

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

     Functions in this group are mainly for supporting purposes and may
     not be of any use outside the package they reside

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

       
     getRepSourceNBuilt(name, object)
     mapGO2Probe(eg, baseMapType)
     writeReverseMap(annData, pkgName, pkgPath)
     writeAnnData2Pkg(annData, pkgName, pkgPath)
     getAnnData(srcObjs)
     getUniMappings(baseName, eg, ug, otherSrc, baseMapType)
     getBaseFile(baseName)
     getSrcObjs(srcUrls, baseName, organism, baseMapType = c("gb", "ug",
     "ll", "image", "refseq", "gbNRef"), fromWeb = TRUE)
     cleanSrcObjs(srcObjs)
     mapll2PathID(srcUrl, organism, exten = "gene_map.tab")
     mapLLNGB(organism, pkgName, pkgPath, ugUrl = getSrcUrl("ug", organism),
     egUrl = paste(getSrcUrl("eg"), "gene2accession.gz"), fromWeb = TRUE) 
     getLLNGBMap(repList, what = "ll2gb")
     mapUGNGB(organism, pkgName, pkgPath, ugUrl = getSrcUrl("ug", organism),
     llUrl = getSrcUrl("ll"), fromWeb = TRUE)
     getRepList4Perl(organism, ugUrl = getSrcUrl("ug", organism), llUrl =
     getSrcUrl("ll"), fromWeb = TRUE) 
     getTaxid(organism)

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

   ugUrl: 'ugUrl' a character string for the url to the ftp site of
          UniGene

   llUrl: 'llUrl' a character string for the url to the ftp site of
          LocusLink

   egUrl: 'egUrl' a character string for the url to the ftp site of
          Entrez Gene

 repList: 'repList' a list with values to be used to replace contents
          in template files

    name: 'name' a character string for the name a data source to be
          used to build a data package

  object: 'object' an object that is a subclass of pubRepo

      ll: 'll' an object of class LL

      ug: 'ug' an object of class ug

baseMapType: 'baseMapType' a character string for the type of base map
          (e. g. gb, ug, ll, ...)

 annData: 'annData' a matrix derived from source data

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

 pkgPath: 'pkgPath' a character string for the path where a new package
          will be built

 srcObjs: 'srcObjs' a list containing objects of class UG, LL, GO and
          so on

baseName: 'baseName' a character string for the nam of a base file to
          be used to build a data package

otherSrc: 'otherSrc' a named vector for files contianing mappings
          between probe ids and LocusLink ids obtained by other sources

 srcUrls: 'srcUrls' a named vector for the urls to the source data to
          be used to build data packages

  srcUrl: 'srcUrl' a url for a source data file to be used

 fromWeb: 'fromWeb' a boolean indicating whether a source url is a real
          url or just the path to a locally stored file

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

   exten: 'exten' a character string for the extension to be appended
          to the end of a given url to make the url complete

    what: 'what' a character string that can either be ll2gb or gb2ll

      eg: 'eg' an EG object

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

     Jianhua Zhang

