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 'cellHTS'
     object.  The names of the files, plus additional information
     (plate number, repeat number, assay/treatment/condition) 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.

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

importFun: a function to read the data files.  The default function
          works for a certain file format, such as that of the example
          files provided with this package.  If your plate reader
          software produces files with a different format, the import
          function needs to be adapted. See details.

 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 named 'Filename', 'Plate', and 'Replicate'.
     The contents of the columns 'Plate' and 'Replicate' are expected
     to be integers. The optional 'Batch' column can be used to supply
     batch information for an experiment, e.g., when a reagent has been
     changed or the experiment has been run over several days.

     Further columns are allowed, and can be used to denote, for
     example, different variants of the assay, treatments, incubation
     times, conditions, etc.

     'importFun' can be used to define a custom function to import data
     files. The 'importFun' function should accept as its first
     argument names from the 'Filename' column of the file table (which
     in principle do not need to be individual files, they could also
     be handles for database entries or pointers into relevants parts
     of a file). It should return a list with two components:



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



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

           *  'val', the intensity values measured in that well.


        and with as many rows as there are wells in the plate.   .ti * 
        The second component 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', since it will be used to reproduce the intensity
        files that are linked in the HTML quality reports generated by
        'writeReport'.


     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 run 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: information about the runs, infered from the 'plateList'
          file: which replicate, which variant of the assay, treatment,
          incubation times etc.

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, Florian
     Hahne

_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)

