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 given
     '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. Useful when the files
          are locate in the same directory,  but should be omitted
          otherwise.

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

_c_o_n_f_F_i_l_e 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 data.frame
     with at least three columns named 'Plate', 'Well' and 'Content'.
     Columns 'Plate' and 'Well' are allowed to contain regular
     expressions. For more details about the plate configuration file,
     read the accompanying vignette.

_l_o_g_F_i_l_e If given as an argument, 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.


_d_e_s_c_r_i_p_F_i_l_e This file is the screen description file with general
     information about the screen.

     Data from wells that are annotated as _empty_ are ignored and are
     set to NA in 'object' in slot 'xraw'.

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

     An S4 object of class 'cellHTS', which extends the class
     'NChannelSet'. The followings slots of 'object' are updated: 

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 having 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'

_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)

