convertCel            package:affxparser            R Documentation

_C_o_n_v_e_r_t_s _a _C_E_L _i_n_t_o _t_h_e _s_a_m_e _C_E_L _b_u_t _w_i_t_h _a_n_o_t_h_e_r _f_o_r_m_a_t

_D_e_s_c_r_i_p_t_i_o_n:

     Converts a CEL into the same CEL but with another format.
     Currently only CEL files in version 4 (binary/XDA) can be written.
     However, any input format is recognized.

_U_s_a_g_e:

     convertCel(filename, outFilename, readMap=NULL, writeMap=NULL, version="4", ..., .validate=FALSE, verbose=FALSE)

_A_r_g_u_m_e_n_t_s:

filename: The pathname of the original CEL file.

outFilename: The pathname of the destination CEL file. If the same as
          the source file, an exception is thrown.

 readMap: An optional read map for the input CEL file.

writeMap: An optional write map for the output CEL file.

 version: The version of the output file format.

     ...: Not used.

.validate: If 'TRUE', a consistency test between the generated and the
          original CDF is performed.  Note that the memory overhead for
          this can be quite large, because two complete CDF structures
          are kept in memory at the same time.

 verbose: If 'TRUE', extra details are written while processing.

_V_a_l_u_e:

     Returns (invisibly) 'TRUE' if a new CEL was generated, otherwise
     'FALSE'.

_B_e_n_c_h_m_a_r_k_i_n_g _o_f _A_S_C_I_I _a_n_d _b_i_n_a_r_y _C_E_L_s:

     Binary CELs are much faster to read than ASCII CELs.  Here are
     some example for reading complete CELs (the differnce is even
     larger when reading CELs in subsets):

        *  To do

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

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

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

     'createCel'().

_E_x_a_m_p_l_e_s:

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

     # Search for some available Calvin CEL files
     path <- system.file("rawData", package="AffymetrixDataTestFiles")
     files <- findFiles(pattern="[.](cel|CEL)$", path=path, recursive=TRUE, firstOnly=FALSE)
     files <- grep("FusionSDK_Test3", files, value=TRUE)
     files <- grep("Calvin", files, value=TRUE)
     file <- files[1]

     outFile <- file.path(tempdir(), gsub("[.]CEL$", ",XBA.CEL", basename(file)))
     if (file.exists(outFile))
       file.remove(outFile)
     convertCel(file, outFile, .validate=TRUE)

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

