genefilter            package:genefilter            R Documentation

_A _f_u_n_c_t_i_o_n _t_o _f_i_l_t_e_r _g_e_n_e_s.

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

     'genefilter' filters genes in the array 'expr' using the filter
     functions in 'flist'. It returns an array of logical values
     (suitable for subscripting) of the same length as there are rows
     in 'expr'. For each row of 'expr' the returned value is 'TRUE' if
     the row passed all the filter functions. Otherwise it is set to
     'FALSE'.

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

     genefilter(expr, flist)

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

    expr: A matrix or 'exprSet' that the filter functions will be
          applied to. 

   flist: A list of filter functions to apply to the array. 

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

     This package uses a very simple but powerful protocol for
     _filtering_ genes. The user simply constructs any number of tests
     that they want to apply. A test is simply a function (as
     constructed using one of the many helper functions in this
     package) that returns 'TRUE' if the gene of interest passes the
     test (or filter) and 'FALSE' if the gene of interest fails.

     The benefit of this approach is that each test is constructed
     individually (and can be tested individually). The tests are then
     applied sequentially to each gene. The function returns a logical
     vector indicating whether the gene passed all tests functions or
     failed at least one of them.

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

     A logical vector of length equal to the number of rows of 'expr'.
     The values in that vector indicate whether the corresponding row
     of 'expr' passed the set of filter functions.

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

     R. Gentleman

_S_e_e _A_l_s_o:

     'genefilter', 'kOverA'

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

        set.seed(-1)
        f1 <- kOverA(5, 10)
        flist <- filterfun(f1, allNA)
        exprA <- matrix(rnorm(1000, 10), nc=10)
        ans <- genefilter(exprA, flist)

