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)

