qcBeadLevel            package:beadarray            R Documentation

_G_e_n_e_r_a_t_e _s_i_m_p_l_e _d_i_a_g_n_o_s_t_i_c _p_l_o_t_s _f_o_r _I_l_l_u_m_i_n_a _b_e_a_d _l_e_v_e_l _d_a_t_a

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

     Generate simple diagnostic plots for Illumina bead level data

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

     qcBeadLevel(object, whatToPlot="G", RG=FALSE, log=TRUE, nrow = 100, ncol= 100,
                         colDens=1, colBox=0, html=TRUE,
                         fileName="qcsummary.htm", plotdir=NULL,
                         experimentName=NULL, targets=NULL, ...)

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

  object: a BeadLevelList object

whatToPlot: character string or vector specifying which intensities to
          plot. Possibilities are '"G"', '"Gb"' for single channel data
          and '"G"', '"Gb"', '"R"' and '"Rb"' for two-colour data

      RG: if TRUE, plot R vs G intensities per array.  Default value is
          FALSE.  Only useful for two-channel data

     log: if TRUE log2 intensities are plotted

    nrow: How many rows should the array be divided into (used by
          imageplot)

    ncol: How many columns should the array be divided into (used by
          imageplot)

 colDens: colors for density plots (default is 1)

  colBox: colors for box plot (default is 0)

    html: logical scalar.  If 'TRUE' an html summary page  is
          generated.  If 'FALSE', no summary page is generated.

fileName: name of html summary page.  Default is 'qcsummary.htm'.

 plotdir: optional character string specifying the filepath where the
          plots will be saved.  Defaults to current working directory.

experimentName: name to appear on HTML report (default is NULL).

 targets: data.frame containing smaple information

     ...: further arguments that can be passed to the plotting
          functions.

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

     This function creates boxplots, smoothed histogram (density) plots
     and imageplots of raw bead level intensity data.

     An html page called 'qcsummary.htm' which displays the results, is
     created when 'html=TRUE'.

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

     Matt Ritchie

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

     #data(BLData)
     #qcBeadLevel(BLData)

