gapFilter-methods            package:xps            R Documentation

_G_a_p _F_i_l_t_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     This method initializes the Gap Filter. 
      The 'gapFilter' looks for genes that might usefully discriminate
     between two groups. To do this we look for a gap in the ordered
     expression values. The gap should come in the central portion,
     thus a parameter 'window' is defined to exclude jumps in the
     initial 'window' values and the final 'window' values. 
      The Gap Filter flags all rows with: 'flag = ((gap[i+1] -
     gap[i])/mean >= cutoff)'

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

_A_r_g_u_m_e_n_t_s:

  object: object of class 'PreFilter'.

   value: numeric vector 'c(cutoff, window, trim, epsilon)'.

_D_e_t_a_i_l_s:

     The method 'gapFilter' initializes the following parameters:

         'cutoff':   the cutoff level for the filter.
         'window':   trim value for the ordered expression levels (default is 'window=0.05').
         'trim':     the trim value for trimmed mean (default is 'trim=0').
         'epsilon':  value to replace mean (default is 'epsilon=0.01'):
                     'epsilon > 0': replace mean=0 with epsilon.
                     'epsilon = 0': always set mean=1.

     Note, that for 'epsilon = 0' the filter flags all rows with:
     (gap[i+1] - gap[i]) >= cutoff

_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()
     gapFilter(prefltr) <- c(0.3,0.05,0.0,0.01)
     str(prefltr)

