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, ...)

_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: 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.

     ...: 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
     four columns, and column names 'Batch', 'Position', 'Well' and
     'Content'. The contents of 'Position' are expected to be integer.

_l_o_g_F_i_l_e This file 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'.

wellAnno: object of class 'factor' of length number of plates x number
          of wells per plate, with five possible levels: _empty_,
          _other_, _neg_, _sample_, and _pos_, indicative of the
          contents of the wells.

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

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

     ..

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

      datadir = system.file("KcViabSmall", package = "cellHTS")
      x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
      confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
      logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
      descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
      x = configure(x, confFile, logFile, descripFile)

