callFilter-methods            package:xps            R Documentation

_D_e_t_e_c_t_i_o_n _C_a_l_l _F_i_l_t_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     Detection Call Filter. 
      The 'cutoff' value defines the upper threshold for allowed
     detection call p-values. If e.g. the number of samples exceeding
     this cutoff value is greater than 'samples' then the corresponding
     expression dataframe row is flagged, i.e. 'flag = 0'. 
      The Detection Call Filter flags all rows with: 'flag =
     (sum(call[i] >= cutoff) >= samples)'

     _Usage_

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

_A_r_g_u_m_e_n_t_s:

  object: object of class 'PreFilter' or 'UniFilter'.

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

_D_e_t_a_i_l_s:

     The method 'callFilter' initializes the following parameters:

         'cutoff':     the cutoff value for the filter:
                       'cutoff = 1.0': present/absent call is used.
                       'cutoff < 1.0': detection p-value is used as cutoff.
         'samples':    this value depends on the 'condition' used:
         'condition':  'condition="samples"': number of samples (default):
                       'condition="percent"': percent of samples.

_V_a_l_u_e:

     An initialized 'PreFilter' or 'UniFilter' object.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_E_x_a_m_p_l_e_s:

     ## initialize PreFilter
     prefltr <- PreFilter()
     callFilter(prefltr) <- c(0.02,80.0,"percent")
     str(prefltr)

     ## initialize UniFilter
     unifltr <- UniFilter()
     callFilter(unifltr) <- c(0.02,80.0,"percent")
     str(unifltr)

