getChroLocation          package:AnnBuilder          R Documentation

_F_u_n_c_t_i_o_n_s _t_o _e_x_t_r_a_c_t _d_a_t_a _f_r_o_m _G_o_l_d_e_n _P_a_t_h

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

     These functions are used by objects GP to extract chromosomal
     location and orientation data for genes using source files
     provided by Golden Path

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

     getChroLocation(srcUrl, exten = gpLinkNGene(), sep = "\t", fromWeb =
     TRUE, raw = FALSE)
     getGPData(srcUrl, sep = "\t")
     gpLinkNGene(test = FALSE, fromWeb = TRUE)
     getCytoList(data)
     getCytoLoc(organism, srcUrl = paste(getSrcUrl("gp",organism), "/",
               "http://www.genome.ucsc.edu/goldenPath/mm4/database/" ))

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

  srcUrl: 'srcUrl' a character string for the url where Golden Path
          source data are available

   exten: 'exten' a character string for the name of the file to be
          used for the extraction

     sep: 'sep' a character string for the separator used by the source
          file

    test: 'test' a boolean to indicate whether the process is in a
          testing mode

 fromWeb: 'fromWeb' a boolean to indicate whether the source data
          should be downloaded from the web or is a local file

     raw: 'raw' a boolean indicating whether chromosomal location data
          will be returned as a five column data frame with ID,
          Chromosome, strand, start, and end or a two column data with
          ID and processed chromosome location data

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

    data: 'data' a data matrix

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

     'getChroLocation' extracts chromosomal location data from a data
     file named refGene.

     'getGPData' Reads data from a source data file defined by srcUrl
     and returns them as a matrix.

     'gpLinkNGene' returns a correct link and gene data file names that
     will be used to get chromosomal location data.

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

     'getChroLocation' returns a matrix with five or two columns.

     'getGPData' returns a matrix.

     'gpLinkNGene' returns a named vector.

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

     Jianhua Zhang

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

     <URL: http://www.genome.ucsc.edu>

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

     'GP'

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

     ## Not run: 
     # Truncated versions of files stored in Bioconductor site are used
     gpLinkNGene(test = FALSE)
     temp <- getGPData(
     "http://www.bioconductor.org/datafiles/wwwsources/Tlink.txt",
     sep = "\t", ncol = 8, keep = c(3,7))
     temp <- getChroLocation(
     "http://www.bioconductor.org/datafiles/wwwsources/",
     exten = gpLinkNGene(TRUE), sep = "\t")
     ## End(Not run)

