read.Galfile           package:marrayInput           R Documentation

_R_e_a_d_i_n_g _G_e_n_e_P_i_x _G_a_l _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Reading a standard Gal file containing gene information.

_U_s_a_g_e:

     read.Galfile(galfile, path = ".", info.id = c("Name", "ID"),
     labels = "ID", notes = galfile, sep = "\t", skip = NULL, quote = "\"",
     fill=TRUE, ncolumns=4, ...)

_A_r_g_u_m_e_n_t_s:

 galfile: a character string representing the Gal file.

    path: a character string representing the data directory. By
          default this is set to the current working directory ("."). 

 info.id: the column numbers in `fname' that contain the required
          information.

  labels: the column number in 'fname' which contains the names that
          the user would like to use to label spots or arrays (e.g. for
          default titles in 'maPlot'.

   notes: object of class character, vector of explanatory text

     sep: the field separator character.  Values on each line of the
          file are separated by this character. The default is to read
          a tab delimited file.

    skip: the number of lines of the data file to skip before beginning
          to read data.

   quote: the set of quoting characters. By default, this is disable by
          setting `quote=""'.

    fill: logical: if `TRUE', `scan' will implicitly add empty fields
          to any lines with fewer fields than implied by `what'.

ncolumns: an integer representing the number of columns of sub-array
          (print-tips) on a slides.

     ...: further arguments to 'scan'.

_V_a_l_u_e:

  gnames: An object of class 'marrayInfo'.

  layout: An object of class 'marrayLayout'.

_A_u_t_h_o_r(_s):

     Yee Hwa (Jean) Yang

_S_e_e _A_l_s_o:

     'read.marrayInfo', 'read.marrayLayout'

_E_x_a_m_p_l_e_s:

     library(marrayInput)
     datadir <- system.file("data", package="marrayInput")
     try <- read.Galfile(galfile="fish.gal", path=datadir)
     names(try)
     try$layout
     try$gnames

