readCcg              package:affxparser              R Documentation

_R_e_a_d_s _a_n _A_f_f_y_m_e_t_r_i_x _C_o_m_m_a_n_d _C_o_n_s_o_l_e _G_e_n_e_r_i_c (_C_C_G) _D_a_t_a _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Reads an Affymetrix Command Console Generic (CCG) Data file.  The
     CCG data file format is also known as the Calvin file format.

_U_s_a_g_e:

     readCcg(pathname, verbose=0, .filter=NULL, ...)

_A_r_g_u_m_e_n_t_s:

pathname: The pathname of the CCG file.

 verbose: An 'integer' specifying the verbose level. If 0, the file is
          parsed quietly.  The higher numbers, the more details.

 .filter: A 'list'.

     ...: Not used.

_D_e_t_a_i_l_s:

     Note, the current implementation of this methods does not utilize
     the Affymetrix Fusion SDK library.  Instead, it is implemented in
     R from the file format definition [1].

_V_a_l_u_e:

     A named 'list' structure consisting of ...

_A_b_o_u_t _t_h_e _C_C_G _f_i_l_e _f_o_r_m_a_t:

     A CCG file, consists of a "file header", a "generic data header",
     and "data" section, as outlined here:

        *  File Header

        *  Generic Data Header (for the file)

           1.  Generic Data Header (for the files 1st parent)

              1.  Generic Data Header (for the files 1st parents 1st
                 parent)

              2.  Generic Data Header (for the files 1st parents 2nd
                 parent)

              3.  ...

              4.  Generic Data Header (for the files 1st parents Mth
                 parent)

           2.  Generic Data Header (for the files 2nd parent)

           3.  ...

           4.  Generic Data Header (for the files Nth parent)

        *  Data

           1.  Data Group #1

              1.  Data Set #1 \itemize {

              2.  Parameters

              3.  Column definitions

              4.  Matrix of data }

              5.  Data Set #2

              6.  ...

              7.  Data Set #L

           2.  Data Group #2

           3.  ...

           4.  Data Group #K

_A_u_t_h_o_r(_s):

     Henrik Bengtsson (<URL: http://www.braju.com/R/>)

_R_e_f_e_r_e_n_c_e_s:

     [1] Affymetrix Inc, Affymetrix GCOS 1.x compatible file formats,
     April, 2006. <URL: http://www.affymetrix.com/support/developer/>

_S_e_e _A_l_s_o:

     'readCcgHeader'(). 'readCdfUnits'().

