PreFilter-constructor          package:xps          R Documentation

_C_o_n_s_t_r_u_c_t_o_r _f_o_r _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:

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

_U_s_a_g_e:

     PreFilter(mad         = character(),
               cv          = character(),
               variance    = character(),
               difference  = character(),
               ratio       = character(),
               gap         = character(),
               lothreshold = character(),
               hithreshold = character(),
               quantile    = character(),
               prescall    = character())

_A_r_g_u_m_e_n_t_s:

     mad: '"character"' vector describing parameters for 'madFilter'.

      cv: '"character"' vector describing parameters for 'cvFilter'.

variance: '"character"' vector describing parameters for 'varFilter'.

difference: '"character"' vector describing parameters for
          'diffFilter'.

   ratio: '"character"' vector describing parameters for 'ratioFilter'.

     gap: '"character"' vector describing parameters for 'gapFilter'.

lothreshold: '"character"' vector describing parameters for
          'lowFilter'.

hithreshold: '"character"' vector describing parameters for
          'highFilter'.

quantile: '"character"' vector describing parameters for
          'quantileFilter'.

prescall: '"character"' vector describing parameters for 'callFilter'.

_D_e_t_a_i_l_s:

     The PreFilter constructor allows to apply the following filters to
     class 'ExprTreeSet':

         'mad':          character vector c(cutoff,epsilon).
         'cv':           character vector c(cutoff,trim,epsilon).
         'variance':     character vector c(cutoff,trim,epsilon).
         'difference':   character vector c(cutoff,trim,epsilon).
         'ratio':        character vector c(cutoff).
         'gap':          character vector c(cutoff,window,trim,epsilon).
         'lothreshold':  character vector c(cutoff,parameter,condition).
         'hithreshold':  character vector c(cutoff,parameter,condition).
         'quantile':     character vector c(cutoff,loquantile,hiquantile).
         'prescall':     character vector c(cutoff,samples,condition).

_V_a_l_u_e:

     An object of type '"PreFilter"'

_N_o_t_e:

     Function 'PreFilter' is used as constructor for class 'PreFilter'
     so that the user need not know details for creating S4 classes.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'Filter', 'UniFilter'

_E_x_a_m_p_l_e_s:

     ## fill character vectors within constructor
     prefltr <- PreFilter(mad=c(0.5,0.01), prescall=c(0.002, 6,"samples"),
                          lothreshold=c(6.0,0.02,"mean"), hithreshold=c(10.5,80.0,"percent"))
     str(prefltr)

     ## alternatively add character vectors as methods after creation of constructor
     prefltr <- PreFilter()
     madFilter(prefltr) <- c(0.5,0.01)
     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")
     str(prefltr)

