configure              package:cellHTS              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:

     configure(x, ...)
     ## S3 method for class 'cellHTS':
     configure(x, confFile, logFile, descripFile, path, ...)

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

       x: a 'cellHTS' object.

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.

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.

    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.

     ...: additional parameters - ignored.

_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 at
        least three columns, and column names 'Batch', 'Well' and
        'Content'. The contents of 'Batch' are expected to be integer. 

   _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 'Filename', 'Well', and 'Flag'. 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 'x' in slot 'xraw'.

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

     An S3 object of class 'cellHTS', which extends the argument 'x' by
     the following elements: 

plateConf: a data.frame containing what was read from input file
          'confFile'. The number of rows is equal to the product
          between the number of wells in each plate and the number of
          batches.

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'.

wellAnno: object of class 'factor' of length number of plates x number
          of wells per plate, with possible levels: _empty_, _other_,
          _neg_, _sample_, and _pos_, indicative of the contents of the
          wells. Other levels may be employed for the positive and
          negative controls, besides _pos_ and _neg_.


     There are methods 'print.cellHTS', 'configure.cellHTS' and
     'annotate.cellHTS'.

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

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

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

     ..

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

     'readPlateData'

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

     ## Not run: 
         datadir <- system.file("KcViabSmall", package = "cellHTS")
         x <- readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
         x <- configure(x, "Plateconf.txt", "Screenlog.txt", "Description.txt", path=datadir)
     ## End(Not run)

