beadAnalysis          package:BeadExplorer          R Documentation

_A_u_t_o_m_a_t_e_d _B_e_a_d _A_n_a_l_y_s_i_s

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

     A function to easily automate standard qc and normalisation
     analyses of BeadStudio output data

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

     beadAnalysis(datafile = NULL, qcdatafile = NULL, version, qc = "ArrayQuality.txt", output = "png", normalise = "Quantile", 
     bkd="Offset", offset=NULL, outputhtml = TRUE, open = TRUE, manifest="", outputsamples = TRUE, 
     outputarrays = TRUE, outputresults = TRUE, return = "Normalised", widget = TRUE)

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

datafile: A character vector of a filepath(s) of Illumina BeadStudio
          'gene profile.csv' output files 

qcdatafile: A character vector of a filepath(s) of Illumina BeadStudio
          "qcinfo.csv" output files 

 version: A character vector, either "one or "two" indicating the
          version of BeadStduio used to create the QC data file 

      qc: A character of the path to a log file of previously analysed
          data, as created by Bead Explorer 

  output: A character specifying output types for graphs.  Options are
          "png", "bmp", "jpeg" 

normalise: A character specifying a normalisation option.  Options are
          "Quantile", "Qspline", "RobustQuantile"

     bkd: A character spcificying the background adjustment method. 
          Options are "Offset" or "Base"

  offset: A numeric specifiying the offset value to add

outputhtml: A logical specifying whether a html report should be
          produced 

    open: A logical specifying whether the html report should be opened

manifest: Character specifying the path of the Illumina manifest .csv
          file to use.  Adds annotation information to the output
          results file

outputsamples: A logical specifying whether a sample QC graph should be
          produced

outputarrays: A logical specifying whether an array QC graph should be
          produced 

outputresults: A logical specifying whether a normalised results file
          should be produced 

  return: A character specifying a return option.  Options are "Raw",
          "Normalised", "None"

  widget: A logical specifying whether a widget should be used for
          input 

_D_e_t_a_i_l_s:

     This is a wrapper function that automates the analysis of
     BeadStudio output files.  Note that the input data can be created
     using version one or  version two of BeadStudio - this must be
     specified.  See vignette for details of widget. All output files
     will be placed in the current working directory.  By submitting
     multiple separate files, the data will be combined into one
     analysis.  Use default values to run a human example data set.

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

     The return value is determined by the return argument:
     'Normalised' returns a normalised 'beadData-class' object,  'Raw'
     - an unnormalised 'beadData-class' object, 'None' - NULL

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

     Gareth Elvidge gareth.elvidge@well.ox.ac.uk

_S_e_e _A_l_s_o:

     'normalise', 'dotplotArrays',  'plotSamples', 'help'

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

     ## Not run: 
     data<-beadAnalysis()
     ## End(Not run)

