printTopGenes             package:lemma             R Documentation

_L_E_M_M_A - _p_r_i_n_t_i_n_g _t_h_e _m_o_s_t _l_i_k_e_l_y _n_o_n_n_u_l_l _g_e_n_e_s

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

     This program prints `topgenes' genes sorted in ascending order by
     their  posterior null probability, or by their adjusted p-value.
     Use a positive integer, or `all' to print all the genes, or
     `nonnull' to print only the genes that are declared nonnull with
     the given local fdr or FDR cut-off values.  It is executed by
     'lemma()', but can be executed later separately, if the user wants
     to print a different number of `topgenes', without running the EM
     algorithm again.

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

       printTopGenes(type, outdir, data0, data1, data2, geneid, genename,
          topgenes, titletext, cutoff, modes)

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

    type: Either `RR' or `FDR'.

  outdir: The directory with the AllData.RData file from a previous
          invocation of 'lemma()'. The output files will be stored in
          the outdir directory (overwriting the previous copy).

   data0: Enter RRfdr0 if type=`RR', or pBH0 if type=`FDR'

   data1: Enter RRfdr1 if type=`RR', or (dg-tau) if type=`FDR'

   data2: Enter (dg-tau) if type=`RR', or c() if type=`FDR'

  geneid: Use the geneid vector

genename: Use the genename vector

topgenes: the number of genes to print (sorted in ascending order by
          local-fdr or adjusted p-value). Use `all' to print all the
          genes, or `nonnull' to print only the genes that are declared
          nonnull with the given local fdr or FDR cut-off values.
          Default=`nonnull'.

titletext: The title to be used in the output files.

  cutoff: Enter locfdrcutoff if type=`RR', or fdrcutoff if type=`FDR'

   modes: the number of assumed (null + nonnull) groups. Can be either
          2 or 3 (default=3)

