highFilter-methods            package:xps            R Documentation

_U_p_p_e_r _T_h_r_e_s_h_o_l_d _F_i_l_t_e_r

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

     This method initializes the Upper Threshold Filter. 
      The 'cutoff' value defines the upper threshold for allowed
     expression levels. If e.g. the number of samples exceeding this
     cutoff value is greater than 'parameter' then the corresponding
     dataframe row is flagged, i.e. 'flag = 0'. 
      The Upper Threshold Filter flags all rows with: 'flag =
     (sum(expression[i] <= cutoff) >= parameter)'

     _Usage_

     'highFilter(object)' 
      'highFilter(object, value)<-'

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

  object: object of class 'PreFilter'.

   value: character vector 'c(cutoff, parameter, condition)'.

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

     The method 'highFilter' initializes the following parameters:

         'cutoff':     the upper threshold level for the filter.
         'parameter':  this value depends on the 'condition' used:
         'condition':  'condition="samples"':    number of samples (default):
                       'condition="percent"':    percent of samples.
                       'condition="mean"':       mean value of samples.
                       'condition="percentile"': percentile of samples.

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

     An initialized 'PreFilter' object.

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

     Christian Stratowa

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

     prefltr <- PreFilter()
     highFilter(prefltr) <- c(14.5,75.0,"percent")
     str(prefltr)

