findCdf              package:affxparser              R Documentation

_S_e_a_r_c_h _f_o_r _C_D_F _f_i_l_e_s _i_n _m_u_l_t_i_p_l_e _d_i_r_e_c_t_o_r_i_e_s

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

     Search for CDF files in multiple directories.

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

     findCdf(chipType=NULL, paths=NULL, recursive=TRUE, pattern="[.](c|C)(d|D)(f|F)$", ...)

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

chipType: A 'character' string of the chip type to search for.

   paths: A 'character' 'vector' of paths to be searched. The current
          directory is always searched at the beginning. If 'NULL',
          default paths are searched.  For more details, see below.

recursive: If 'TRUE', directories are searched recursively.

 pattern: A regular expression file name pattern to match.

     ...: Additional arguments passed to 'findFiles'().

_D_e_t_a_i_l_s:

     Note, the current directory is always searched first, but never
     recursively (unless it is added to the search path explicitly).
     This provides an easy way to override other files in the search
     path.

     If 'paths' is 'NULL', then a set of default paths are searched.
     The default search path consitutes:

        1.  'getOption("AFFX_CDF_PATH")'

        2.  'Sys.getenv("AFFX_CDF_PATH")'

     One of the easiest ways to set system variables for R is to set
     them in an '.Renviron' file, e.g.


         # affxparser: Set default CDF path

     AFFX_CDF_PATH=${AFFX_CDF_PATH};M:/Affymetrix_2004-100k_trios/cdf

     AFFX_CDF_PATH=${AFFX_CDF_PATH};M:/Affymetrix_2005-500k_data/cdf

     See 'Startup' for more details.

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

     Returns a 'vector' of the full pathnames of the files found.

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

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

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

     This method is used internally by 'readCelUnits'() if the CDF file
     is not specified.

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

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

     # Find a specific CDF file
     cdfFile <- findCdf("Mapping10K_Xba131")
     print(cdfFile)

     # Find the first CDF file (no matter what it is)
     cdfFile <- findCdf()
     print(cdfFile)

     # Find all CDF files in search path and display their headers
     cdfFiles <- findCdf(firstOnly=FALSE)
     for (cdfFile in cdfFiles) {
       cat("=======================================\n")
       hdr <- readCdfHeader(cdfFile)
       str(hdr)
     }

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

