geneFilter            package:ArrayTools            R Documentation

_f_i_l_t_e_r _a_n _E_x_p_r_e_s_s_i_o_n_S_e_t _u_s_i_n_g _d_i_f_f_e_r_e_n_t _m_e_t_h_o_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     Create a filtered 'ExpressionSet' based on background, range, or
     interquartile range

_U_s_a_g_e:

     geneFilter(object, pct = 0.1, numChip = ceiling(ncol(exprs(object)) * pct), bg = 4, range = 0, iqrPct = 0, output = FALSE, mydir = getwd())

_A_r_g_u_m_e_n_t_s:

  object: an 'ExpressionSet'

     pct: percentage

 numChip: number of chips. If you would like to filter the
          'ExpressionSet'  based on at least 3 chips greater than 1
          (bg=1), then set numChip = 3

      bg: background value. If you would like to filter the
          'ExpressionSet' based on at least 3 chips greater than 1,
          then set bg=1

   range: range = max value - min value of each gene

  iqrPct: interquartile percentage

  output: if output = TRUE, output filtered data in the sepecified
          directory 

   mydir: the directory containing the filtered data

_D_e_t_a_i_l_s:

     There are three filtering methods. The User can use either one,
     two, or three.  1). At least a certain number of chips (numChip)
     are greater than a given background (bg) 2). The range of the gene
     have to be greater than a given value (range) 3). Calulating the
     interquatile range (IQR) of each gene to create an IQR vector. 
     Based on the given percentage (e.g. iqrPct=0.2), find the
     corresponding percentile.  If IQR is less than percentile, the
     gene will be filtered

_V_a_l_u_e:

     a filtered 'ExpressionSet'

_A_u_t_h_o_r(_s):

     Xiwei Wu, Arthur Li

_E_x_a_m_p_l_e_s:

     data(eSetExample)
     filtered <- geneFilter(eSetExample)

