mboxplot-methods             package:xps             R Documentation

_B_o_x _P_l_o_t_s _o_f _R_e_l_a_t_i_v_e _M _V_a_l_u_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Produce boxplots of relative M values for the set of arrays.

     _Usage_

     ' mboxplot(x, which = "", size = 0, transfo = log2, method  =
     "mean", range = 0, ylim = c(-1,1), outline = FALSE, names =
     "namepart", ...) '

_A_r_g_u_m_e_n_t_s:

       x: object of class 'DataTreeSet' or 'ExprTreeSet'.

   which: type of probes to be used, for details see 'validData'.

    size: length of sequence to be generated as subset.

 transfo: a valid function to transform the data, usually "log2", or
          "0".

  method: method to create the reference data, "mean" or "median".

   range: determines how far the plot whiskers extend out from the box.

    ylim: range for the plotted y values.

 outline: if 'outline' is not true, the outliers are not drawn.

   names: optional vector of sample names.

     ...: optional arguments to be passed to 'boxplot'.

_D_e_t_a_i_l_s:

     Create boxplots of M plots, where M is determined relative to a
     pseudo-mean reference chip.

     For 'names=NULL' full column names of slot 'data' will be
     displayed while for  'names="namepart"' column names will be
     displayed without name extension. If 'names' is a vector of column
     names, only these columns will displayed as boxplot.

_N_o_t_e:

     For a 'DataTreeSet' object, data must first be attached using
     method  'attachInten'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'boxplot.dev', 'boxplot'

_E_x_a_m_p_l_e_s:

     # load existing ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     # need to attach scheme mask and probe intensities
     data.test3 <- attachMask(data.test3)
     data.test3 <- attachInten(data.test3)

     if (interactive()) {
     mboxplot(data.test3, ylim=c(-6,6))
     }

     # optionally remove mask and data to free memory
     data.test3 <- removeInten(data.test3)
     data.test3 <- removeMask(data.test3)

