readPlateData            package:cellHTS            R Documentation

_R_e_a_d _a _c_o_l_l_e_c_t_i_o_n _o_f _p_l_a_t_e _r_e_a_d_e_r _d_a_t_a _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Reads a collection of plate reader data files into a data.frame.
     The names of the files, plus additional information (plate number,
     repeat number) is expected in a tab-delimited table specified by
     the argument 'x'.

_U_s_a_g_e:

     readPlateData(filename, path=dirname(filename), name, plateType="384", verbose=TRUE)

_A_r_g_u_m_e_n_t_s:

filename: the name of the file table (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.

    name: a character of length 1 with the experiment name.

    path: a character of length 1 indicating the path in which to find
          the plate reader files. By default,  it can extract the path
          from 'filename'.

plateType: a character of length 1, allowed values are "96" and "384".

 verbose: a logical value, if TRUE, the function reports some of its
          intermediate progress.

_D_e_t_a_i_l_s:

     The file table is expected to be a tab-delimited file with at
     least three columns, and column names 'Filename', 'Plate', and
     'Replicate'. The contents of the columns 'Plate' and 'Replicate'
     are expected to be integers. Further columns are allowed.

     We distinguish between _plates_ and _plate result file_. A plate
     result file contains the measurements results for all replicates
     and all channels of a plate, which is the physical carrier of the
     reagents.

_V_a_l_u_e:

     An object of class '"cellHTS"', which is currently implemented as
     a list with elements 

    name: copy of the input argument 'name'

    xraw: an array of dimension plateSize x number of plates x number
          of replicates x number of channels, containg the imported
          measurement data.

    pdim: a numeric vector of length 2 containg the number of rows and
          columns in a plate. The product of these two numbers is the
          first dimension of 'xraw'.

   batch: an integer vector with the batch number (1, 2, ...) for each
          plate. Its length corresponds to the second dimension of  of
          'xraw'.

plateList: a data.frame containing what was read from input file 'x',
          plus a column 'status' of type character: it contains the
          string "OK" if the data import appeared to have gone well,
          and the respective error or warning message otherwise.

intensityFiles: a list of character vectors, each containing a copy of
          the imported input data files. Its length corresponds to the
          number of rows of 'plateList'.

   state: a logical vector representing the processing status of the
          object.

_A_u_t_h_o_r(_s):

     W. Huber huber@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)

