SAFE-class               package:safe               R Documentation

_C_l_a_s_s _S_A_F_E

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

     The class SAFE is the output from the function 'safe'. It is also
     the input    to the plotting function 'safeplot'.

_S_l_o_t_s:


     '_l_o_c_a_l': Object of class '"character"' describing the local
          statistic used.

     '_l_o_c_a_l._s_t_a_t': Object of class '"numeric"' containing the
          (unsorted) observed local statistics for genes.

     '_l_o_c_a_l._p_v_a_l': Object of class '"numeric"' containing the
          (unsorted) empirical p-values for genes

     '_g_l_o_b_a_l': Object of class '"character"' describing the local
          statistic used.

     '_g_l_o_b_a_l._s_t_a_t': Object of class '"numeric"' containing the
          (unsorted) observed global statistics for categories.

     '_g_l_o_b_a_l._p_v_a_l': Object of class '"numeric"' containing the
          (unsorted) empirical p-values for categories.

     '_e_r_r_o_r': Object of class '"character"' describing the method used
          to estimate error rates across multiple comparisons.

     '_g_l_o_b_a_l._e_r_r_o_r': Object of class '"numeric"' containing the
          (unsorted) error rates associated with the p-values for
          categories. If not computed,  it will be set to 'NA'.

     '_C._m_a_t': Object of class '"matrix"' containing the category
          assignments. Each row corresponds to a gene, and each column
          a category.

     '_a_l_p_h_a': Object of class '"numeric"' containing the alpha level
          for significance of a category.

     '_m_e_t_h_o_d': Object of class '"character"' describing the resampling 
          method used in 'safe'.

_M_e_t_h_o_d_s:


     _s_h_o_w (gt.result): Summarizes the test results of significant
          categories.

     [ (gt.result): Returns a SAFE object for categories indicated by
          integer of character strings.

     _s_a_f_e_p_l_o_t (gt.result): The 'safeplot' produces a plot of the
          relative association of expression in a category of genes
          relative to their complement.

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

     William T Barry: bill.barry@duke.edu

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

     'safe', 'safeplot'.

