findDelta              package:siggenes              R Documentation

_F_i_n_d_i_n_g _t_h_e _T_h_r_e_s_h_o_l_d _D_e_l_t_a

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

     Computes the value of the threshold Delta for a given FDR or
     number of genes/variables in a SAM or EBAM analysis.

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

        findDelta(object, fdr = NULL, genes = NULL, prec = 6, initial = NULL,
           verbose = FALSE)

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

  object: either a SAM or an EBAM object.

     fdr: numeric value between 0 and 1 for which the threshold Delta
          and thus the number of genes/variables should be obtained.
          Only one of 'fdr' and 'genes' can be specified.

   genes: integer specifying the number of genes/variables for which
          the threshold Delta and thus the estimated FDR should be
          obtained. Only one of 'fdr' and 'genes' can be specified.

    prec: integer indicating the precision of the considered Delta
          values.

 initial: a numeric vector of length two containing the minimum and the
          maximum value of Delta that is initially used in the search
          for Delta. Both values must be larger than 0. If 'object' is
          an EBAM object, both values must also be smaller than or
          equal to 1. If not specified, the minimum is set to 0.1, and
          the maximum to either the maximum posterior (EBAM) or the
          maximum absolute distance between the observed and the
          corresponding expected values of the test statistic (SAM).

 verbose: should more information about the search process be shown?

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

     If a value of Delta is found for the exact value of 'fdr' or
     'genes', then a vector of length 3 consisting of Delta and the
     corresponding number of genes and the estimated FDR. If such a
     value is not found, then a matrix with two rows and three columns,
     where the two rows contain the number of genes/variables and the
     estimated FDR for the two considered values of Delta that provide
     the closest upper and lower bounds to the desired FDR (if 'fdr' is
     specified) or number of genes/variables (if 'genes' is specified.)

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

     Holger Schwender, holger.schwender@udo.edu

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

     'sam', 'ebam'

