readGAL                package:limma                R Documentation

_R_e_a_d _a _G_A_L _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Read a GenePix Array List (GAL) file into a dataframe.

_U_s_a_g_e:

     readGAL(galfile=NULL,path=NULL,header=TRUE,sep="\t",quote="\"",skip=NULL,as.is=TRUE,...)

_A_r_g_u_m_e_n_t_s:

 galfile: character string giving the name of the GAL file.  If 'NULL'
          then a file with extension '.gal' is found in the directory
          specified by 'path'.

    path: character string giving the directory containing the files. 
          If 'NULL' then assumed to be the current working directory.

  header: logical variable, if 'TRUE' then the first line after 'skip'
          is assumed to contain column headings.  If 'FALSE' then a
          value should specified for 'skip'.

     sep: the field separator character

   quote: the set of quoting characters

    skip: number of lines of the GAL file to skip before reading data. 
          If 'NULL' then this number is determined by searching the
          file for column headings.

   as.is: logical variable, if 'TRUE' then read in character columns as
          vectors rather than factors.

     ...: any other arguments are passed to 'read.table'

_D_e_t_a_i_l_s:

     A GAL file is a list of genes IDs and associated information
     produced by an Axon microarray scanner. Apart from header
     information, the file must contain data columns labeled 'Block',
     'Column', 'Row' and 'ID'. A 'Name' column is usually included as
     well. Other columns are optional. See the Axon URL below for a
     detaile description of the GAL file format.

     This function reads in the data columns with a minimum of user
     information. In most cases the function can be used without
     specifying any of the arguments.

_V_a_l_u_e:

     A data frame with columns 

   Block: numeric vector containing the print tip indices

  Column: numeric vector containing the spot columns

     Row: numeric vector containing the spot rows

      ID: character vector, for factor if 'as.is=FALSE', containing
          gene library identifiers

    Name: character vector, for factor if 'as.is=FALSE', containing
          gene names

     The data frame will be sorted so that 'Column' is the fastest
     moving index, then 'Row', then 'Block'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.axon.com/gn_GenePix_File_Formats.html>

_S_e_e _A_l_s_o:

     An overview of LIMMA functions for reading data is given in
     03.ReadingData.

_E_x_a_m_p_l_e_s:

     # readGAL()
     # will read in the first GAL file (with suffix ".gal")
     # found in the current working directory