qcPlots             package:tilingArray             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 _A_f_f_y_m_e_t_r_i_x _t_i_l_i_n_g _a_r_r_a_y _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Generate simple diagnostic plots for Affymetrix tiling array data

_U_s_a_g_e:

     qcPlots(x, html=TRUE, plotdir=NULL, probeAnno, gff, 
                         chr=4, coord=c(230000,245000),
                         nr = 2560, nc = 2560,
                         ylimchrom=c(5,16), nucleicAcid, pmindex, pgm=TRUE,
                         ext=".cel", ranks=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

       x: ExpressionSet containing the data to be plotted.

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

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

probeAnno: environment with probe annotations. See package
          'davidTiling' for an example (?probeAnno).

     gff: data frame with genome annotation from the GFF file.

     chr: integer of length 1 indicating the chromosome number to plot.

   coord: integer vector of length 2 containing the start and end
          coordinates (in bases) for the along chromosome intensity
          plot.

      nr: integer, indicating the number of probes in each row on the
          array (2560 for yeast tiling arrays).

      nc: integer, indicating the number of probes in each column on
          the array (2560 for yeast tiling arrays).

ylimchrom: numeric vector containing the y limits of the along
          chromosome intensity plot.

nucleicAcid: character vector or factor indicating what sample has been
          hybridised to each array. Used to color the boxplots and
          smoothed histograms of intensities.

 pmindex: integer vector of indices of PM probes in 'x'.  If missing,
          this information is extracted from 'probeAnno'.

     pgm: logical scalar.  If 'TRUE', image plots will be saved as .pgm
          files.  Otherwise ('FALSE'), they are converted to jpegs. On
          windows machines, this argument should be set to 'TRUE'.

     ext: character string indicating the file extension.

   ranks: logical scalar.  If 'TRUE', imageplots will show ranks of
          standardised probe intensities.  Otherwise ('FALSE',
          default), the standardised probe intensities are plotted.

     ...: further arguments that can be passed to the plotting function
          'plotSegmentationDots'.

_D_e_t_a_i_l_s:

     This function creates boxplots, smoothed histogram (density)
     plots, imageplots and  along chromosome plots of the raw (log base
     2) probe intensity data.

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

     Imageplots of standardised intensities (i.e. (probe intensity -
     minimum probe intensity) divided by the difference between the
     maximum and minimum probe intensities, all on log base 2 scale) or
     the ranks of these standardised intensities are plotted depending
     on the 'ranks' argument. 

     The individual plots are named by replacing the file extension
     (specified by 'ext') of each 'celfile.ext', with 'density.png' for
     smoothed histogram plots, 'gencoord.jpg', for along chromosome
     plots and either 'log.pgm' ('log.jpg' if 'pgm=FALSE') or
     'rank.pgm' ('rank.jpg' if 'pgm=FALSE') for the imageplots,
     depending on the 'ranks' argument.

_A_u_t_h_o_r(_s):

     Matt Ritchie <ritchie@ebi.ac.uk> and Wolfgang Huber
     <huber@ebi.ac.uk>

_E_x_a_m_p_l_e_s:

     ## library(davidTiling)
     ## data(davidTiling)
     ## data(probeAnno)
     ## qcPlots(davidTiling, probeAnno)
      

