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"), flat=FALSE, 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.

    flat: Do we want a flat return.

 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 element of the list is in turn a 'list'
     structure with three components: 

  groups: A 'list' with one component for each group (also called
          block). The information on each group is a 'list' with five
          components: 'x', 'y', 'pbase', 'tbase', 'expos', and
          'indices'.

    type: An 'integer' specifying the type of the unit, where 1 is
          "expression", 2 is "genotyping", 3 is "CustomSeq", and 4
          "tag".

direction: An 'integer' specifying the direction of the unit, which
          defines if the probes are interrogating the sense or the
          anti-sense target, where 0 is "no direction", 1 is "sense",
          and 2 is "anti-sense".

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'readCdfUnits'().

