import.data               package:xps               R Documentation

_I_m_p_o_r_t _C_E_L _f_i_l_e_s _i_n_t_o _a _D_a_t_a_T_r_e_e_S_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     Import the Affymetrix CEL files into a ROOT file and create S4
     class DataTreeSet

_U_s_a_g_e:

     import.data(xps.scheme,
                 filename = character(0),
                 filedir  = getwd(),
                 celdir   = NULL,
                 celfiles = "*",
                 celnames = NULL,
                 project  = NULL,
                 verbose  = TRUE)

_A_r_g_u_m_e_n_t_s:

xps.scheme: a 'SchemeTreeSet' containing the correct scheme for the
          CEL-files

filename: file name of ROOT data file.

 filedir: system directory where ROOT data file should be stored.

  celdir: system directory containing the CEL-files for corresponding
          scheme.

celfiles: optional vector of CEL-files to be imported.

celnames: optional vector of names which should replace the CEL-file
          names.

 project: optional class 'ProjectInfo'.

 verbose: logical, if 'TRUE' print status information.

_D_e_t_a_i_l_s:

     'import.data' is used to import CEL-files from directory 'celdir'
     into  a 'ROOT' data file. To import only a subset of CEL-files,
     list these CEL-files  as vector 'celfiles'.

     To import CEL-files from different directories, vector 'celfiles'
     must contain the full path for each CEL-file and 'celdir' must be
     'celdir=NULL'. 

     Currently, the following types of Affymetrix CEL-files can be
     imported:  text (version 3), xml, binary (xda), generic
     (agcc,calvin)

     An S4 class 'DataTreeSet' will be created, serving as R wrapper to
     the  'ROOT' data file 'filename'.

     Use function 'root.data' to access the 'ROOT' data file from new R
     sessions to avoid creating a new 'ROOT' data file for every
     session.

_V_a_l_u_e:

     A 'DataTreeSet' object.

_N_o_t_e:

     As mentioned above, use function 'root.data' to access the  ROOT
     data file from new R sessions to avoid creating a new 'ROOT' data
     file  for every R session.

     Do not separate 'filename' of ROOT files with dots, use
     underscores, e.g. do not use  'filename="Data.Test3"' but use
     'filename="Data_Test3"' or 'filename="DataTest3"' instead.

     To every ROOT data file the extension "_cel" is attached to
     'filename' to easily recognize ROOT data files containing the raw
     CEL data, e.g. for 'filename="Data_Test3"' the final name is
     "Data_Test3_cel.root". Extension "root" is added automatically, so
     that ROOT is able to recognize the file as ROOT file.

     Once a 'ROOT' file is created it can not be overwritten, it must
     be deleted manually first. Only 'ROOT' files called "tmp" or with
     'filename'  starting with "tmp_" will be re-created automatically.

     If CEL-file names contain dots and/or colons as characters, these
     characters will be replaced by underscores. It is recommended to
     use parameter 'celnames' to create shorter CEL names and to
     replace special characters.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'root.data', 'DataTreeSet'

_E_x_a_m_p_l_e_s:

     ## get scheme and import CEL-files from package
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- import.data(scheme.test3,"tmp_data_test3",celdir=paste(.path.package("xps"),"raw",sep="/"))
     unlist(treeNames(data.test3))

     ## import only subset of CEL-files
     subdata.test3 <- import.data(scheme.test3,"tmpdt_data_test3",celdir=paste(.path.package("xps"),"raw",sep="/"),
                      celfiles=c("TestA1.CEL","TestB2.CEL"),verbose=FALSE)
     unlist(treeNames(subdata.test3))

