readCdfCellIndices        package:affxparser        R Documentation

_R_e_a_d_s _c_e_l_l _i_n_d_i_c_e_s _o_f _u_n_i_t_s (_p_r_o_b_e_s_e_t_s) _i_n _a_n _A_f_f_y_m_e_t_r_i_x _C_D_F _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Reads cell indices of units (probesets) in an Affymetrix CDF file.

_U_s_a_g_e:

     readCdfCellIndices(filename, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"), verbose=0)

_A_r_g_u_m_e_n_t_s:

filename: The filename of the CDF file.

   units: An 'integer' 'vector' of unit indices specifying which units
          to be read.  If 'NULL', all units are read.

stratifyBy: A 'character' string specifying which and how elements in
          group fields are returned. If '"nothing"', elements are
          returned as is, i.e. as 'vector's. If '"pm"'/'"mm"', only
          elements corresponding to perfect-match (PM) / mismatch (MM)
          probes are returned (as 'vector's). If '"pmmm"', elements are
          returned as a matrix where the first row holds elements
          corresponding to PM probes and the second corresponding to MM
          probes.  Note that in this case, it is assumed that there are
          equal number of PMs and MMs; if not, an error is generated.
          Moreover, the PMs and MMs may not even be paired, i.e. there
          is no guarantee that the two elements in a column corresponds
          to a PM-MM pair.

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

_V_a_l_u_e:

     A named 'list' where the names corresponds to the names of the
     units read.  Each unit element of the list is in turn a 'list'
     structure with one element 'groups' which in turn is a 'list'. 
     Each group element in 'groups' is a 'list' with a single field
     named 'indices'.  Thus, the structure is


          cdf
           +- unit #1
           |   +- "groups"
           |       +- group #1
           |       |   +- "indices"
           |       |  group #2
           |       |   +- "indices"
           |       .
           |       +- group #K
           |           +- "indices"
           +- unit #2
           .
           +- unit #J

     This is structure is compatible with what 'readCdfUnits'()
     returns.

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'readCdfUnits'().

