boxplotBeads            package:beadarray            R Documentation

_B_o_x _p_l_o_t _o_f _b_e_a_d _i_n_t_e_n_s_i_t_i_e_s

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

     Function to produce box plots of the bead intensities from 
     selected strips/arrays from a 'BeadLevelList' object.

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

     boxplotBeads(BLData, whatToPlot = "G", arrays = NULL, log = TRUE,
               varwidth = TRUE, method = "illumina", n = 3, trim = 0.05, ...)

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

  BLData: 'BeadLevelList'

whatToPlot: character string specifying which intensities to plot. See
          'getArrayData' for a list of the possibilities.

  arrays: integer (scalar or vector) specifying the strips/arrays to
          plot. If 'NULL', all the strips/arrays are plotted.

     log: if TRUE log2 intensities are plotted

varwidth: logical, indicating whether box widths should be proportional
          to the number of values in each box plot

  method: character string specifying the summarisation method to use
          (only applicable when 'whatToPlot="residG"', '"residR"' or
          '"residM"'). Refer to help 'createBeadSummaryData' help page
          for further information.

       n: numeric value defining a cut-off for the number of  median
          absolute deviations (MADs) from the median to use for 
          determining outliers.  The default value is 3.  Only
          applicable when 'whatToPlot="residG"', '"residR"' or
          '"residM"' and 'method="illumina"'.  Refer to help
          'createBeadSummaryData'  help page for further information.

    trim: fraction of intensities to remove from the bead summary
          calculations. Only applicable when 'whatToPlot="residG"',
          '"residR"' or '"residM"'.  Refer to 'createBeadSummaryData'
          help page for further information.

     ...: further graphical parameters to the 'boxplot' function from
          the graphics package

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

     Produces box plots of the specified intensities for selected
     strips/arrays.

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

     A plot is produced on the current graphical device

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

     Matt Ritchie

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

     data(BLData)

     boxplotBeads(BLData)

