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", newChipType = NULL, ..., .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.

newChipType: An optional string for overriding the chip type in the CEL
          file header.

     ...: Not used.

.validate: If 'TRUE', a consistency test between the generated and the
          original CEL is performed.

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

