lowFilter-methods            package:xps            R Documentation

_L_o_w_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 Lower Threshold Filter. The 'cutoff'
     value defines the lower threshold for allowed expression levels.
     If e.g. the number of samples lower than this cutoff value is
     greater than 'parameter' then the corresponding dataframe row is
     flagged, i.e. 'flag = 0'. 
      The Lower Threshold Filter flags all rows with: 'flag =
     (sum(expression[i] >= cutoff) >= parameter)'

     _Usage_

     'lowFilter(object)' 
      'lowFilter(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 'lowFilter' initializes the following parameters:

         'cutoff':     the lower 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()
     lowFilter(prefltr) <- c(4.0,3,"samples")
     str(prefltr)

