readHTAnalystData          package:cellHTS2          R Documentation

_R_e_a_d _a _s_e_t _o_f _p_l_a_t_e _r_e_s_u_l_t_s _o_b_t_a_i_n_e_d _f_r_o_m _a _H_T_a_n_a_l_y_s_e_r _p_l_a_t_e _r_e_a_d_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     Reads input files (specified by the argument 'filenames')
     containing replicate data for the same set of assay plates and
     obtained using an HTanalyser.   The number of replicates
     corresponds to the number of given files ('length(filenames)'),
     while the total number of plates should be given by the argument
     'nrPlates'.

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

     readHTAnalystData(filenames, path=dirname(filenames), name, nrPlates, verbose=interactive())

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

filenames: vector of characters giving the name(s) of the input file(s)
          obtained in a HTanalyser plate reader and containing the set
          of measurements for each set of replicate plates (see
          details).

    path: can be either a character vector with the same length as
          'filenames' or a character of length 1 indicating the path in
          which to find the input file(s) 'filenames'. By default,  it
          can extract the path from 'filenames'.

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

nrPlates: an integer value indicating the number of plates in the input
          file(s).

 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:

     This function reads input files obtained in a HTanalyser plate
     reader for a multi-plate format screening experiment. Data for the
     same set of replicate measurements of all plates are expected to
     come in a single input file. So, the argument 'filenames' should
     be a character vector specifying the name of the input files for
     each replicate. Each of these files is expected to contain data
     for a total of 'nrPlates' assay plates. It contains
     meta-experimental data together with plate measurements in a
     matrix-like format. The same type of format is expected for each
     of the 'nrPlates' contained in each input file indicated in
     'filenames'. The input files should be suitable to be used as
     input for 'readLines'.

     The following metadata fields are expected to be repeated along
     the input file(s) for each assay plate:

        *  Microplate format, indicates the plate format used in the
           screen. Should be the same across plates.

        *  Barcode, this field is used to uniquely identify each assay
           plate.

        *  Method ID, indicates the method used to perform the assay.
           Should be the same for every plate.

        *  Data, indicates the type of data and should be the same for
           every plate.

        *  Units, indicates the units of the readings. Should be the
           same for every plate.

        *  Display format, indicating the numeric format used to
           display the data measurements. Should be the same along
           plates.

     This function expects that the next line after the meta field
     "Display format" for a given plate contains the column numbers
     ('1:ncol') which are then followed by the matrix of measurements
     in each well. Each entry of the data matrix corresponds to a
     position in the assay plate with coordinates '(row, col)', except
     the first column, which gives the row ID, as upper letters (A, B,
     ...).

_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.

intensityFiles: a list, where each component contains a copy of the
          measurement data of a given plate, replicate and channel. Its
          length corresponds to the number of rows of 'plateList'.

plateList: a data.frame containing the columns "Filename", "Plate",
          "Replicate", "Channel" and "status". Each row of this slot
          makes the correspondence between a given component (name
          given in column "Filename") in the list stored in slot
          'intensityFiles' (i.e. plate) and its respective plate,
          replicate and channel number. Thus, this data.frame contains
          as many rows as the product between the total number of
          plates, replicates and channels. The last column named
          'status' is of type character and contains the string "OK"
          indicated the success status of the data import.

_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 a collection of plate result files with measurements of a
     single plate and replicate, see 'readPlateList'.

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

         datadir <- system.file("KcCellTiter", package = "cellHTS2")
         x <- readHTAnalystData(filenames = c("KcCellTiter0607.txt", "KcCellTiter0707.txt"), name="KcData", path=datadir, nrPlates=3L)
         x <- configure(x, confFile = "Plateconf.txt", logFile="Screenlog.txt", descripFile = "Description.txt",
                path = datadir)

