readQC               package:beadarray               R Documentation

_R_e_a_d _I_l_l_u_m_i_n_a _q_u_a_l_i_t_y _c_o_n_t_r_o_l _i_n_f_o_r_m_a_t_i_o_n

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

     Reads the standard format of Illumina quality control information
     and produces diagnostic plots

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

     readQC(file, columns = list(exprs = "AVG_Signal", NoBeads = "Avg_NBEADS", Detection="Detection", BeadStDev="BEAD_STDERR", Narrays="NARRAYS", arrayStDev = "ARRAY_STDEV", controlID = "ProbeID", controlType="TargetID"),sep="\t",skip=7,header=T)

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

    file: name of file containing qc information

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

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

  header: if TRUE the column names in the file are read

     sep: a character string for the file separator

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

     The format of the quality control files differs slightly between
     BeadStudio versions 1 and 2. Version 1 of the software gives one
     averaged value for each control type, whereas version 2 gives
     suumarised values for each control of a particular type. The user
     does not have to know the version of BeadStudio used to generate
     the file.

     Once read in, the quality control information can be very useful
     for diagnostic purposes.

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

     readQC produces an assayData object with list items defined by the
     columns parameter.

_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(sep=",", skip=7, columns=list(exprs="AVG.Signal", BeadStDev="SeqVAR"))

     #the average expression of each control can then be accessed by the $ operator

     #QC$exprs

