readQC               package:beadarray               R Documentation

_R_e_a_d _I_l_l_u_m_i_n_a _c_o_n_t_r_o_l _i_n_t_e_n_s_i_t_i_e_s

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

     Reads the standard format of Illumina control intensities output
     by BeadStudio

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

     readQC(file, sep="\t", skip=8, controlID = "ProbeID", columns = list(exprs = "AVG_Signal", se.exprs="BEAD_STDERR", NoBeads = "Avg_NBEADS", Detection="Detection Pval"), dec=".", quote="")

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

    file: character string giving the name of the file output by
          BeadStudio containing the control probe intensities.  This
          file should be either the 'ControlProbeProfile' or
          'ControlGeneProfile'.

     sep: a character string for the file separator

    skip: number of lines of header information to ignore in the file

controlID: character string specifying the column that contains the 
          (unique) control probe IDs

 columns: a vector of column names to read from the file

     dec: the character used in the file for decimal points

   quote: the set of quoting characters (disabled by default)

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

     The format of the quality control files differs slightly between
     BeadStudio  versions 1 and later versions.  This function is able
     to read in data  in either format

     Note that if the control identifiers are non-unique, the
     duplicated  rows are removed.  This may occur if the
     'ControlProbeProfile' is  exported from BeadStudio and
     'controlID="TargetID"' is specified  (the "ProbeID" column has a
     unique identifier in the 'ControlProbeProfile', whereas the
     "TargetID" may not, as multiple beads can be of the same type).

     Once read in, the control intensities can be used for quality
     assessment purposes.

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

     'readQC' produces an 'assayData' object with a list of items
     defined  by the 'columns' parameter.  The row names of each matrix
     are given by the  'controlID' argument .

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

     Mark Dunning

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

     ##Code to read the example quality control file included with the
     #package.
     #QC = readQC("ControlGeneProfile.txt", controlID="TargetID")
     #the average expression of each control can then be accessed by the $ operator
     #QC$exprs

