readCelIntensities        package:affxparser        R Documentation

_R_e_a_d_s _t_h_e _i_n_t_e_n_s_i_t_i_e_s _c_o_n_t_a_i_n_e_d _i_n _s_e_v_e_r_a_l _A_f_f_y_m_e_t_r_i_x _C_E_L _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Reads the intensities of several Affymetrix CEL files (as opposed
     to 'readCel'() which only reads a single file).

_U_s_a_g_e:

      readCelIntensities(filenames, indices = NULL, ..., verbose = 0)

_A_r_g_u_m_e_n_t_s:

filenames: the names of the CEL files as a character vector.

 indices: a vector of which indices should be read. If the argument is
          'NULL' all features will be returned.

     ...: Additional arguments passed to 'readCel'().

 verbose: an integer: how verbose do we want to be, higher means more
          verbose.

_D_e_t_a_i_l_s:

     The function will initially allocate a matrix with the same memory
     footprint as the final object.

_V_a_l_u_e:

     A matrix with a number of rows equal to the length of the
     'indices' argument (or the number of features on the entire chip),
     and a number of columns equal to the number of files. The columns
     are ordered according to the 'filenames' argument.

_N_o_t_e:

     Currently this function builds on 'readCel'(), and simply calls
     this function multiple times. If testing yields sufficient reasons
     for doing so, it may be re-implemented in C++.

_A_u_t_h_o_r(_s):

     James Bullard, bullard@stat.berkeley.edu and Kasper Daniel Hansen,
     khansen@stat.berkeley.edu

_S_e_e _A_l_s_o:

     'readCel'() for a discussion of a more versatile function,
     particular with details of the 'indices' argument.

_E_x_a_m_p_l_e_s:

       # Scan current directory for CEL files
       files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
       if (length(files) >= 2) {
         cel <- readCelIntensities(files[1:2])
         str(cel)
         rm(cel)
       }

       # Clean up
       rm(files)

