sumSAM-class            package:siggenes            R Documentation

_C_l_a_s_s_e_s _s_u_m_S_A_M _a_n_d _s_u_m_E_B_A_M

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

     These classes are just used for a nicer output of the summary of
     an object of class SAM or EBAM, respectively.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("sumSAM", ...)',
     or by using the function 'summary(object)' when object is a 
     SAM-class object.  

     Objects can be created by calls of the form 'new("sumEBAM", ...)',
     or by using the function 'summary(object)' when object is an 
     EBAM-class object.

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


     '_r_o_w._s_i_g._g_e_n_e_s': Object of class '"numeric"' consisting of the row
          numbers of the significant genes in the data matrix.

     '_m_a_t._f_d_r': Object of class '"matrix"' containing general
          information as the number of differentially expressed genes
          and the estimated FDR for either one or several values of
          Delta.

     '_m_a_t._s_i_g': Object of class '"data.frame"' containing gene-specific
          statistics as the d-values (or z-values) and the q-values or
          (the local FDR) of the differentially expressed genes.

     '_l_i_s_t._a_r_g_s': Object of class '"list"' consisting of some of the
          specified arguments of summary needed for internal use.

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


     _p_r_i_n_t 'signature(x = "sumSAM")': Prints the output of the
          SAM-specific method summary.

     _s_h_o_w 'signature(object = "sumSAM")': Shows the output of the
          summary of a SAM analysis.

     _p_r_i_n_t 'signature(x = "sumEBAM")': Prints the output of the
          EBAM-specific method summary.

     _s_h_o_w 'signature(object = "sumEBAM")': Shows the output of the
          summary of a EBAM analysis.

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

     Holger Schwender, holger.schw@gmx.de

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

     'SAM-class', 'EBAM-class'

