readCdfDataFrame         package:affxparser         R Documentation

_R_e_a_d_s _u_n_i_t_s (_p_r_o_b_e_s_e_t_s) _f_r_o_m _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 units (probesets) from an Affymetrix CDF file. Gets all or a
     subset of units (probesets).

_U_s_a_g_e:

     readCdfDataFrame(filename, units=NULL, groups=NULL, cells=NULL, fields=NULL, drop=TRUE, 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 are read.

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

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

  fields: A 'character' 'vector' specifying what fields to read. If
          'NULL', all unit, group and cell fields are returned.

    drop: If 'TRUE' and only one field is read, then a 'vector' (rather
          than a single-column 'data.frame') is returned.

 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:

     An NxK 'data.frame' or a 'vector' of length N.

_R_e_f_e_r_e_n_c_e_s:

     [1] Affymetrix Inc, Affymetrix GCOS 1.x compatible file formats,
     June 14, 2005. <URL: http://www.affymetrix.com/support/developer/>

_S_e_e _A_l_s_o:

     For retrieving the CDF as a 'list' structure, see
     'readCdfUnits'().

_E_x_a_m_p_l_e_s:

     ##############################################################
     if (require("AffymetrixDataTestFiles")) {            # START #
     ##############################################################

     # Find any CDF file
     cdfFile <- findCdf()

     units <- 101:120
     fields <- c("unit", "unitName", "group", "groupName", "cell")
     df <- readCdfDataFrame(cdfFile, units=units, fields=fields)
     stopifnot(identical(sort(unique(df$unit)), units))

     fields <- c("unit", "unitName", "unitType")
     fields <- c(fields, "group", "groupName")
     fields <- c(fields, "x", "y", "cell", "pbase", "tbase")
     df <- readCdfDataFrame(cdfFile, units=units, fields=fields)
     stopifnot(identical(sort(unique(df$unit)), units))

     ##############################################################
     }                                                     # STOP #
     ##############################################################

