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 #
     ##############################################################

