Plot.genes           package:GlobalAncova           R Documentation

_M_e_t_h_o_d_s _f_o_r _F_u_n_c_t_i_o_n _P_l_o_t._g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     There are three possible ways of using 'GlobalAncova', use
     'methods ? GlobalAncova' for getting more information. Also
     'Plot.genes' can be invoked with these three alternatives.

_M_e_t_h_o_d_s:

     _x_x = "_m_a_t_r_i_x", _f_o_r_m_u_l_a._f_u_l_l = "_f_o_r_m_u_l_a", _f_o_r_m_u_l_a._r_e_d = "_f_o_r_m_u_l_a", _m_o_d_e_l._d_a_t = "_A_N_Y", _g_r_o_u_p = "_m_i_s_s_i_n_g", _c_o_v_a_r_s = "_m_i_s_s_i_n_g", _t_e_s_t._t_e_r_m_s = "_m_i_s_s_i_n_g" 
          In this method, besides the expression matrix 'xx', model
          formulas for the full and reduced model and a data frame
          'model.dat' specifying corresponding model terms have to be
          given. Terms that are included in the full but not in the
          reduced model are those whose association with differential
          expression will be tested. The arguments 'group', 'covars'
          and 'test.terms' are '"missing"' since they are not needed
          for this method.

     _x_x = "_m_a_t_r_i_x", _f_o_r_m_u_l_a._f_u_l_l = "_f_o_r_m_u_l_a", _f_o_r_m_u_l_a._r_e_d = "_m_i_s_s_i_n_g", _m_o_d_e_l._d_a_t = "_A_N_Y", _g_r_o_u_p = "_m_i_s_s_i_n_g", _c_o_v_a_r_s = "_m_i_s_s_i_n_g", _t_e_s_t._t_e_r_m_s = "_c_h_a_r_a_c_t_e_r" 
          In this method, besides the expression matrix 'xx', a model
          formula for the full model and a data frame 'model.dat'
          specifying corresponding model terms are required. The
          character argument 'test.terms' names the terms of interest
          whose association with differential expression will be
          tested. The arguments 'formula.red', 'group' and 'covars' are
          '"missing"' since they are not needed for this method.

     _x_x = "_m_a_t_r_i_x", _f_o_r_m_u_l_a._f_u_l_l = "_m_i_s_s_i_n_g", _f_o_r_m_u_l_a._r_e_d = "_m_i_s_s_i_n_g", _m_o_d_e_l._d_a_t = "_m_i_s_s_i_n_g", _g_r_o_u_p = "_A_N_Y", _c_o_v_a_r_s = "_A_N_Y", _t_e_s_t._t_e_r_m_s = "_m_i_s_s_i_n_g" 
          Besides the expression matrix 'xx' a clinical variable
          'group' is required. Covariate adjustment is possible via the
          argument 'covars' but more complex models have to be
          specified with the methods described above. This method
          emulates the function call in the first version of the
          package. The arguments 'formula.full', 'formula.red',
          'model.dat' and 'test.terms' are '"missing"' since they are
          not needed for this method.

