readCdf              package:affxparser              R Documentation

_P_a_r_s_i_n_g _a _C_D_F _f_i_l_e _u_s_i_n_g _A_f_f_y_m_e_t_r_i_x _F_u_s_i_o_n _S_D_K

_D_e_s_c_r_i_p_t_i_o_n:

     This function parses a CDF file using the Affymetrix Fusion SDK.

     _This function will most likely be replaced by the more general
     'readCdfUnits()' function._

_U_s_a_g_e:

      readCdf(filename, units=NULL, 
              readXY=TRUE, readBases=TRUE, 
              readIndexpos=TRUE, readAtoms=TRUE, 
              readUnitType=TRUE, readUnitDirection=TRUE, 
              readUnitNumber=TRUE, readUnitAtomNumbers=TRUE, 
              readGroupAtomNumbers=TRUE, readGroupDirection=TRUE, 
              readIndices=FALSE, readIsPm=FALSE, 
              stratifyBy=c("nothing", "pmmm", "pm", "mm"), 
              verbose=0)

_A_r_g_u_m_e_n_t_s:

filename: name of the CDF file.

 verbose: how verbose should the output be. 0 means no output, with
          higher numbers being more verbose.

_V_a_l_u_e:

     A list with one component for each unit. Every component is again
     a list with three components     

  groups: This is again a list with one component for each group (also
          called block). The information on each group is a list with 5
          components, 'x', 'y', 'pbase', 'tbase', 'expos'.

    type: type of the unit.

direction: direction of the unit.

_N_o_t_e:

     This version of the function does not return information on the QC
     probes. This will be added in a (near) future release. In addition
     we expect the header to be part of the returned object.

     So expect changes to the structure of the value of the function in
     next release. Please contact the developers for details.

_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:

     'readCdfHeader()' for getting the header of a CDF file.

