yeastPkgBuilder          package:AnnBuilder          R Documentation

_F_u_n_c_t_i_o_n_s _t_o _d_o _a _d_a_t_a _p_a_c_k_a_g_e _f_o_r _y_e_a_s_t _g_e_n_o_m_e

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

     These functions builds a data package for yeast genome using data
     from Yeast Genome web site of Stanford University, KEGG, and Gene
     Ontology.

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

     yeastPkgBuilder(pkgName, pkgPath, base = "", srcUrls = c(YG =
                      getSrcUrl("YG"), KEGG = getSrcUrl("KEGG", organism =
                      "Saccharomyces cerevisiae"), GO = getSrcUrl("GO")),
                      version = "1.1.0",
                      makeXML = TRUE, author = list(author = "who",
                      maintainer = "who@email.com"), fromWeb = TRUE)

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

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

    base: 'base' a matrix with two columns with the first one being
          probe ids and the second one being their mappings to ORF
          (Open Reading Frame) ids. Columns have the name "probe" and
          "orf"

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

 srcUrls: 'srcUrls' a named vector of strings for the urls for KEGG
          (<URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways>) and GO
          (http://www.godatabase.org/dev/database/archive/2003-05-01/go
          _200305-termdb.xml.gz). The urls may change over time

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

 makeXML: 'makeXML' a boolean to indicate whether an XML version of the
          data will be generated

  author: 'author' a named vector of two character strings with a name
          element for the name and an address element of email address
          of the maintainer of the data package

 fromWeb: 'fromWeb' a boolean to indicate whether the data from GO
          should be downloaded from the web or read locally. The url
          for GO should be the file name of a local file if fromWeb is
          FALSE. For windows users, the data file from GO should be
          downloaded/unzipped manually and set the url for GO to be the
          name of the local file

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

     Annotation elements are limited to those provided by Yeast Genome
     (gene name, chromosome number, chromosomal location, GO id, and
     evidence code), KEGG (path and enzyme data) and GO (GO mappings)

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

     'findYGChrLength' returns a named vector of integers with
     chromosome numbers names and length of chromosomes as values.

_N_o_t_e:

     The functions are 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.yeastgenome.org>

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

     # Not provided. 

