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, 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.

 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 at the beginning.
     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 is consituted of:

        1.  '"."'

        2.  '"cdf/;data/cdf/"'

        3.  'getOption("AFFX_CDF_PATH")'

        4.  '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:

     # Find a specific CDF file
     cdfFile <- findCdf("Mapping50K_Xba240")
     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)
     }

