configure              package:cellHTS2              R Documentation

_C_o_n_f_i_g_u_r_e_s _t_h_e _p_l_a_t_e_s _a_n_d _p_l_a_t_e _r_e_s_u_l_t _f_i_l_e_s

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

     Annotate the plates and the plate result files of a 'cellHTS'
     object.

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

     ## S4 method for signature 'cellHTS':
     configure(object, descripFile, confFile, logFile, path)

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

  object: a 'cellHTS' object.

descripFile: the name of the screen description file (see details).
          This argument is just passed on to the 'readLines' function,
          so any of the valid argument types for 'readLines' are valid
          here, too.

confFile: the name of the configuration file (see details). This
          argument is just passed on to the 'read.table' function, so
          any of the valid argument types for 'read.table' are valid
          here, too.  Must contain one row for each well and each
          batch.

 logFile: optional; the name of the screen log file (see details). This
          argument is just passed on to the 'read.table' function, so
          any of the valid argument types for 'read.table' are valid
          here, too.

    path: optional; a character of length one indicating the path in
          which to find the configuration files. It can be useful when
          the files are located in the same directory,  and may be
          omitted otherwise.

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

     The configuration has three components:

     _confFile_: This file specifies where the controls are.  This file
     is expected to be a tab-delimited file with two first header rows
     giving the total number of wells and plates in the screen. The
     next rows should be in the form of a spreadsheet table with at
     least three columns named 'Plate', 'Well' and 'Content'. Columns
     'Plate' and 'Well' are allowed to contain regular expressions. 
     Data from wells that are configured as _empty_ will be ignored and
     are set to 'NA' in the data slot 'xraw'.  For an example, and for
     more details, please read the accompanying vignette.

     _logFile_: This optional file allows to flag certain measurements
     as invalid. It is expected to be a tab-delimited file with at
     least three columns, and column names 'Plate', 'Well', and 'Flag'.
     If there are multiple samples (replicates or conditions), a column
     called 'Sample' should also be given. If there are multiple
     channels, a column called 'Channel' must be given. Further columns
     are allowed.

     _descripFile_: The screen description file contains general
     information about the screen.

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

     An S4 object of class 'cellHTS', which is obtained by copying
     'object' and updating the following slots: 

plateConf: a data frame containing what was read from input file
          'confFile' (except the first two header rows).

screenLog: a data frame containing what was read from input file
          'logFile'.

screenDesc: object of class 'character' containing what was read from
          input file 'descripFile'.

   state: the processing status of the 'cellHTS' object is updated in
          to 'state["configured"]=TRUE'.

featureData: the column 'controlStatus' is updated taking into account
          the well annotation given by the plate configuration file.

experimentData: an object of class 'MIAME' containing descriptions of
          the experiment, constructed from the screen description file.

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

     Wolfgang Huber huber@ebi.ac.uk, Ligia Bras ligia@ebi.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of
     cell-based RNAi screens, _Genome Biology_ *7*, R66.

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

     'readPlateList' 'templateDescriptionFile'

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

         datadir <- system.file("KcViabSmall", package = "cellHTS2")
         x <- readPlateList("Platelist.txt", name="KcViabSmall", path=datadir)
         x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt", path=datadir)

