PreFilter-class             package:xps             R Documentation

_C_l_a_s_s _P_r_e_F_i_l_t_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     Class PreFilter allows to apply different filters to class
     'ExprTreeSet', i.e. to the expression level data.frame 'data'.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("PreFilter",
     ...)'. 
      Alternatively, the contructor 'PreFilter' can be used.

_S_l_o_t_s:


     '_m_a_d': Object of class '"list"' describing parameters for
          'madFilter'.

     '_c_v': Object of class '"list"' describing parameters for
          'cvFilter'.

     '_v_a_r_i_a_n_c_e': Object of class '"list"' describing parameters for
          'varFilter'.

     '_d_i_f_f_e_r_e_n_c_e': Object of class '"list"' describing parameters for
          'diffFilter'.

     '_r_a_t_i_o': Object of class '"list"' describing parameters for
          'ratioFilter'.

     '_g_a_p': Object of class '"list"' describing parameters for
          'gapFilter'.

     '_h_i_t_h_r_e_s_h_o_l_d': Object of class '"list"' describing parameters for
          'highFilter'.

     '_l_o_t_h_r_e_s_h_o_l_d': Object of class '"list"' describing parameters for
          'lowFilter'.

     '_q_u_a_n_t_i_l_e': Object of class '"list"' describing parameters for
          'quantileFilter'.

     '_p_r_e_s_c_a_l_l': Object of class '"list"' describing parameters for
          'callFilter'.

     '_n_u_m_f_i_l_t_e_r_s': Object of class '"numeric"' giving the number of
          filters applied.

_E_x_t_e_n_d_s:

     Class '"Filter"', directly.

_M_e_t_h_o_d_s:


     _c_a_l_l_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot
          'prescall'.

     _c_a_l_l_F_i_l_t_e_r<- 'signature(object = "PreFilter", value =
          "character")': replaces  slot 'prescall' with character
          vector c(cutoff, samples, condition).

     _c_v_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot 'cv'.

     _c_v_F_i_l_t_e_r<- 'signature(object = "PreFilter", value = "numeric")':
          replaces  slot 'cv' with numeric vector c(cutoff, trim,
          epsilon).

     _d_i_f_f_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot
          'difference'.

     _d_i_f_f_F_i_l_t_e_r<- 'signature(object = "PreFilter", value = "numeric")':
          replaces  slot 'difference' with numeric vector c(cutoff,
          trim, epsilon).

     _g_a_p_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot 'gap'.

     _g_a_p_F_i_l_t_e_r<- 'signature(object = "PreFilter", value = "numeric")':
          replaces  slot 'gap' with numeric vector c(cutoff, window,
          trim, epsilon).

     _h_i_g_h_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot
          'hithreshold'.

     _h_i_g_h_F_i_l_t_e_r<- 'signature(object = "PreFilter", value =
          "character")': replaces  slot 'hithreshold' with character
          vector c(cutoff, parameter, condition).

     _l_o_w_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot
          'lothreshold'.

     _l_o_w_F_i_l_t_e_r<- 'signature(object = "PreFilter", value =
          "character")': replaces  slot 'lothreshold' with character
          vector c(cutoff, parameter, condition).

     _m_a_d_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot 'mad'.

     _m_a_d_F_i_l_t_e_r<- 'signature(object = "PreFilter", value = "numeric")':
          replaces  slot 'mad' with numeric vector c(cutoff, epsilon).

     _q_u_a_n_t_i_l_e_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot
          'quantile'.

     _q_u_a_n_t_i_l_e_F_i_l_t_e_r<- 'signature(object = "PreFilter", value =
          "numeric")': replaces  slot 'quantile' with numeric vector
          c(cutoff, loquantile, hiquantile).

     _r_a_t_i_o_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot
          'ratio'.

     _r_a_t_i_o_F_i_l_t_e_r<- 'signature(object = "PreFilter", value =
          "numeric")': replaces  slot 'ratio' with numeric vector
          c(cutoff).

     _v_a_r_F_i_l_t_e_r 'signature(object = "PreFilter")': extracts slot
          'variance'.

     _v_a_r_F_i_l_t_e_r<- 'signature(object = "PreFilter", value = "numeric")':
          replaces  slot 'variance' with numeric vector c(cutoff, trim,
          epsilon).

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     related classes 'Filter', 'UniFilter'.

_E_x_a_m_p_l_e_s:

     ## for demonstration purposes only:  initialize all pre-filters
     prefltr <- new("PreFilter")
     madFilter(prefltr) <- c(0.5,0.01)
     cvFilter(prefltr) <- c(0.3,0.0,0.01)
     varFilter(prefltr) <- c(0.6,0.02,0.01)
     diffFilter(prefltr) <- c(2.2,0.0,0.01)
     ratioFilter(prefltr) <- c(1.5)
     gapFilter(prefltr) <- c(0.3,0.05,0.0,0.01)
     lowFilter(prefltr) <- c(4.0,3,"samples")
     highFilter(prefltr) <- c(14.5,75.0,"percent")
     quantileFilter(prefltr) <- c(3.0, 0.05, 0.95)
     callFilter(prefltr) <- c(0.02,80.0,"percent")
     str(prefltr)

