Cdf-class             package:makecdfenv             R Documentation

_C_l_a_s_s _C_d_f

_D_e_s_c_r_i_p_t_i_o_n:

     A class describing the content a Chip Description File.

_D_e_t_a_i_l_s:

     The class 'Cdf' was designed to store the content of Affymetrix's
     Chip Definition Files (CDF). This early class is no longer widely
     used in the package affy. Environments (called 'cdfenvs') are
     preferred to have an efficient mapping between probe set
     identifiers and indexes (needed to access/subset particular probe
     intensities). Unless one needs to access every information
     contained in a CDF file, the 'cdfenvs' will be preferred.

     The following comments are only relevant to someone with interest
     in what is in a CDF file. The name associated to each probe is not
     unique, it corresponds to the gene name. It is very common to have
     a name repeated 40 times (20 perfect matches and 20 mismatches).
     Probes can be grouped by pairs: a perfect match (PM) probe has its
     mismatch (MM) counterpart. The two probes in a pair differ by one
     base (usually located in the middle of the sequence). The
     information relative to this particular base are stored in 'pbase'
     and 'tbase'. At a given position (x,y), having pbase[x,y] ==
     tbase[x,y] means having a MM while having pbase[x,y] != tbase[x,y]
     means having a perfect mismatch if and only if one of the bases is
     A while the other is TRUE, or one is G and the other is C. The
     function  'pmormm' returns 'TRUE' for PMs and 'FALSE' for MMs.

     To know more about the file structure of a CDF file, one has to
     refer to the parsing code (mostly in C).

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     '  new('Cdf','
      '    cdfName      = ...., # Object of class character'
      '    name         = ...., # Object of class matrix'
      '    name.levels  = ...., # Object of class character'
      '    pbase        = ...., # Object of class matrix'
      '    pbase.levels = ...., # Object of class character'
      '    tbase        = ...., # Object of class matrix'
      '    tbase.levels = ...., # Object of class character'
      '    atom         = ...., # Object of class matrix'
      '  )'

_S_l_o_t_s:

     '_c_d_f_N_a_m_e': the CDF name tag. Used to link with the right CEL files

     '_n_a_m_e': Object of class "matrix" of 'factors' for the gene names
          corresponding to the probes.

     '_n_a_m_e._l_e_v_e_l_s': Object of class "character" containing the levels
          corresponding to 'name'. 

     '_p_b_a_s_e': Object of class "matrix" of pbase levels.

     '_p_b_a_s_e._l_e_v_e_l_s': Object of class "character"  containing the levels
          corresponding to 'pbase'. 

     '_t_b_a_s_e': Object of class "matrix" of tbase levels.

     '_t_b_a_s_e._l_e_v_e_l_s': Object of class "character" containing the levels
          corresponding to 'tbase'.  

     '_a_t_o_m': Object of class "matrix" of atom or probe numbers.

_M_e_t_h_o_d_s:

     _a_t_o_m (Cdf): An accesor function for the 'ato,' slot. 

     _a_t_o_m<- (Cdf):  A replacement function for 'atom' slot. 

     _n_a_m_e._l_e_v_e_l_s (Cdf):  An accesor function for the 'name.levels'
          slot. 

     _n_a_m_e._l_e_v_e_l_s<- (Cdf): A replacement function for 'name.levels'
          slot. 

     _p_b_a_s_e (Cdf):  An accesor function for the 'pbase' slot. 

     _p_b_a_s_e<- (Cdf): A replacement function for 'pbase' slot. 

     _p_b_a_s_e._l_e_v_e_l_s (Cdf):  An accesor function for the 'pbase.levels'
          slot. 

     _p_b_a_s_e._l_e_v_e_l_s<- (Cdf): A replacement function for 'pbase.levels'
          slot. 

     _s_h_o_w (Cdf):  renders information about the exprSet in a concise
          way on stdout. 

     _t_b_a_s_e (Cdf):  An accesor function for the 'tbase' slot. 

     _t_b_a_s_e<- (Cdf): A replacement function for 'tbase' slot. 

     _t_b_a_s_e._l_e_v_e_l_s (Cdf):  An accesor function for the 'tbase.levels'
          slot. 

     _t_b_a_s_e._l_e_v_e_l_s<- (Cdf): A replacement function for 'tbase.levels'
          slot. 

_A_u_t_h_o_r(_s):

     L. Gautier <laurent@cbs.dtu.dk>

_S_e_e _A_l_s_o:

     'read.cdffile', 'make.cdf.env', 'make.cdf.package'

