hist-methods               package:xps               R Documentation

_D_e_n_s_i_t_y _E_s_t_i_m_a_t_e

_D_e_s_c_r_i_p_t_i_o_n:

     Plot the density estimates for each sample.

     _Usage_

     ' hist(x, which = "", size = 0, transfo = log2, ylab = "density",
     xlab = "log intensity", type = "l", col = 1:6, ...) '

_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".

    ylab: a title for the y axis.

    xlab: a title for the x axis.

    type: type for the plot.

     col: colors to use for the different arrays.

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

_D_e_t_a_i_l_s:

     Plots the non-parametric density estimates using values contained
     in the columns of  slot 'data'.

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

_N_o_t_e:

     For exon array raw data only a limited number of samples can be
     displayed as density plot due to memory limitations. To display
     all samples it is proposed to use function 'root.density' instead.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_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()) {
     hist(data.test3)
     }

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

