writeHomoXMLData         package:AnnBuilder         R Documentation

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

     HomoloGene maintains a homology XML data file that differes both
     in the format and contents from the old text file version. The
     functions described here parse the file build the homology
     annotation data pacakge based on the source data.

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

     writeHomoXMLData(pkgName = "homology", pkgPath, version, author, url =
     "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build36/homologene.xml.gz")
     writeHGID2Caption(pkgName, pkgPath, hgid2Cap)
     writeHGID2LL(pkgName, pkgPath, hgid2LL)
     writeHomoData(pkgName, pkgPath, homoFile)
     homoXMLParser(fileName)

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

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

 pkgPath: 'pkgPath' a character string for the path to the directory
          where the new data package will be stored

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

  author: 'author' a list of character strings with an author (name of
          the author of the data package) and a maintainer (e-mail of
          the author of the package)

     url: 'url' a character string for the url to the ftp site where
          the HomoloGene XML file is available. The url change with
          different builds. Check the HomoloGene web site for the
          latest one

hgid2Cap: 'hgid2Cap' a matrix containing mappings between HGIDs and
          their textual descriptions

 hgid2LL: 'hgid2LL' a matrix with mappings between HGIDs and LocusLink
          ids

homoFile: 'homoFile' a character string for the name of a file
          containing data for homologous genes

fileName: 'fileName' a character string for the name of the XML file
          downloaded/unzipped from HomoloGene's ftp site

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

     'writeHomoXMLData' calls other functions listed in this help page
     to complete it's tasks. All the other functions are help functions
     that may not of greate interest to users.

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

     The function returns invisible(NA)

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

     Jianhua Zhang

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

     <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene>

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

