athPkgBuilder           package:AnnBuilder           R Documentation

_F_u_n_c_t_i_o_n_s _t_h_a_t _b_u_i_l_d _a_n_n_o_t_a_t_i_o_n _p_a_c_k_a_g_e_s _f_o_r _A_r_b_i_d_o_p_s_i_s

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

     These functions are implemented specifically for building
     annotation data pckages for arabidopsis using the Arabidopsis
     information source (TAIR).

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

     athPkgBuilder(baseName, pkgName, pkgPath, fileExt = list(estAssign =
     "Genes/est_mapping/est.Assignment.Locus", seqGenes =
     "Genes/TAIR_sequenced_genes", go =
     "Genes/Gene_Ontology/ATH_GO_GOSLIM.20040918.txt", aliases =
     "Genes/gene_aliases.20031113", pathway =
     "Pathways/aracyc_dump_20040520.txt", pmid =
     "Genes/Gene_Anatomy/ATH_Anatomy.20040209.txt"), ncols = list(estAssign =
     7, seqGenes = 4, go = 12, aliases = 4, pathway = 4, pmid = 15),
     cols2Keep = list(estAssign = c(3, 6, 7), seqGenes = c(1, 3), go = c(1,
     5, 9), aliases = c(1, 2), pathway = c(1, 3, 4), pmid = c(6, 11)),
     colNames = list(estAssign = c("CHRLOC", "ORI", "ACCNUM"), seqGenes =
     c("ACCNUM", "CHR"), go = c("ACCNUM", "GO", "EVID"), aliases =
     c("ACCNUM", "SYMBOL"), pathway = c("PATH", "ENZYME", "ACCNUM"), pmid =
     c("PMID", "ACCNUM")), version = "1.1.0", makeXML = TRUE, author =
     list(author = "who", maintainer = "who@email.com"), baseUrl =
     "ftp://tairpub:tairpub@ftp.arabidopsis.org/home/tair/")
     getOneMap(map, keyCol)
     procPMIDData(pmid)
     getSrcObjs4Ath()
     readAthData(baseUrl, ext, col2Keep, colNames, ncols)
     mergeDupMatByFirstCol(dupMat, sep = ";")

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

baseName: 'baseName' a character string for the name of the base file
          to be used to build an annotation data package. The base file
          is assumed to have two columns with the first one being probe
          ids and second one being the corresponding TAIR locus ids.

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

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

 fileExt: 'fileExt' a list of character strings for the extension to be
          appended to a base url to form a complete url for a desired
          source data file stored at TAIR's ftp site. Some of the names
          given as default will change with time and need to be updated

   ncols: 'ncols' an integer indicating the total number of columns of
          a given source data file

cols2Keep: 'cols2Keep' a vector of integers indicating which of the
          columns of a given source data file will be retained when the
          source file is read

colNames: 'colNames' a vector of character strings for the names of the
          columns of the source file to be retained

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

 makeXML: 'makeXML' a boolean indicating whether an XML version of the
          data contained in the annotation data package will be created

  author: 'author' a list of character stirngs with an author and
          maintainer element for the name and email address of the
          author

 baseUrl: 'baseUrl' a character string for the base url to TAIRs ftp
          site, The default is <URL:
          ftp://tairpub:tairpub@ftp.arabidopsis.org/home/tair/>

     map: 'map' a matrix containing mappings between probe ids and
          annotation data

  keyCol: 'keyCol' an integer or character string for the name of the
          column in a matrix that contains the keys based on which data
          in the other columns will be merged for duplicated keys

    pmid: 'pmid' a matrix containing mappings between probe ids and
          PubMed ids regarding genes represented by the probe ids

     ext: 'ext' a single string version of 'fileExt'

  dupMat: 'dupMat' a matrix with duplicating values for entries in a
          column defined as keys

     sep: 'sep' a character string for separator to be used when values
          in a matrix are merged based on keys contained in another
          columns

col2Keep: 'col2Keep' a vector of integers indicating which of the
          column of a data file will be kept when a file is read

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

     The annotation data will be extracted from various sources that
     may change in both names and contents. The default values provided
     were correct at the time of implementation but may need updating
     when the function is actually used.

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

     The main function athPkgBuilder returns invisible()

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

     Jianhua Zhang

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

     <URL: http://www.arabidopsis.org>

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

     'ABPkgBuilder'

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

     # No example is provided due to the length of time required to build a package

