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

