readPlateList            package:cellHTS2            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 'filename'.

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

     readPlateList(filename, path=dirname(filename), name, importFun, verbose=interactive())

_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.

    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'.

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

importFun: a function that should be used to read each plate result
          file. The default function works for plate reader data files.
          See details.

 verbose: a logical value, if TRUE, the function reports some of its
          intermediate progress. Defaults to the state of
          'interactive()'.

_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. 

     'importFun' can be used to define other functions to import other
     data files, such as flow cytometry data files, etc. The
     'importFun' function should receive as an input the name of a
     result plate file to read, and return a list with two components:

        *  The first component should be a 'data.frame' with the
           following slots:

           *  'well', a character vector with the well identifier in
              the plate.

           *  'val', the intensity values measured at each well.

        *  The second component of this list should be a character
           vector containing a copy of the imported input data file
           (such as the output of 'readLines'). It should be suitable
           to be used as input for 'writeLines'. 

     For example, to import plate data files from EnVision plate
     reader, set 'importFun=getEnVisionRawData' or
     'importFun=getEnvisionCrosstalkCorrectedData'. See function
     'getEnVisionRawData'.

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

     An object of class 'cellHTS', which extends the class
     'NChannelSet'.  After calling this function, the content of the
     following slots is as follows: 

assayData: an object of class 'AssayData' containing the imported
          measurement data. Each matrix represents a single channel,
          and each sample (replicate) corresponds to a column. Thus,
          the total number of rows in each matrix corresponds to the
          product between the number of wells per plate and the number
          of assay plates.

phenoData: the argument 'name' is stored in its column 'assay'.

featureData: the information about the plate and well identifiers for
          each plate measurement are stored in columns 'plate' and
          'well' of this slot.

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, where each component contains a copy of the
          imported input data files. Its length corresponds to the
          number of rows of 'plateList'.

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

     W. 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:

     To read input files obtained in a HTanalyser plate reader see
     'readHTAnalystData'.

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

         datadir <- system.file("KcViabSmall", package = "cellHTS2")
         x <- readPlateList("Platelist.txt", "KcViabSmall", path=datadir)

        ## To read data files obtained from an EnVision plate reader:
         datadir <- system.file("EnVisionExample", package = "cellHTS2")
         x <- readPlateList("platelist.txt", name="EnVisionEx",
               importFun=getEnVisionRawData, path=datadir)

            ## to get the cross talk corrected data:
            y <- readPlateList("platelist.txt", name="EnVisionEx", 
                importFun=getEnVisionCrosstalkCorrectedData, path=datadir)

