ExprTreeSet-class            package:xps            R Documentation

_C_l_a_s_s _E_x_p_r_T_r_e_e_S_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     This class provides the link to the 'ROOT' expression file and 
     the 'ROOT' trees contained therein. It extends class 'ProcesSet'.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are created using functions 'express', 'summarize'  or
     'normalize', or the specialized functions 'rma', 'mas5'  or
     'mas4'.

_S_l_o_t_s:


     '_e_x_p_r_t_y_p_e': Object of class '"character"' representing the
          exression type,  i.e. 'rma', 'mas5', 'mas4' or 'custom'.

     '_n_o_r_m_t_y_p_e': Object of class '"character"' representing the
          normalization  type, i.e. 'mean', 'median',
          'lowess','supsmu'.

     '_s_c_h_e_m_e': Object of class '"SchemeTreeSet"' providing access to 
          'ROOT' scheme file.

     '_d_a_t_a': Object of class '"data.frame"'. The data.frame can contain
           the data (e.g. expression levels) stored in 'ROOT' data
          trees.

     '_p_a_r_a_m_s': Object of class '"list"' representing relevant
          parameters.

     '_s_e_t_n_a_m_e': Object of class '"character"' representing the name to
          the 'ROOT' file subdirectoy where the 'ROOT' data trees are
          stored, usually 'PreprocesSet'.

     '_s_e_t_t_y_p_e': Object of class '"character"' describing the type of
          treeset stored in 'setname', usually 'preprocess'.

     '_r_o_o_t_f_i_l_e': Object of class '"character"' representing the name 
          of the 'ROOT' data file, including full path.

     '_f_i_l_e_d_i_r': Object of class '"character"' describing the full path
          to the system directory where 'rootfile' is stored.

     '_n_u_m_t_r_e_e_s': Object of class '"numeric"' representing the number of
           'ROOT' trees stored in subdirectoy 'setname'.

     '_t_r_e_e_n_a_m_e_s': Object of class '"list"' representing the names of
          the  'ROOT' trees stored in subdirectoy 'setname'.

_E_x_t_e_n_d_s:

     Class '"ProcesSet"', directly. Class '"TreeSet"', by class
     "ProcesSet", distance 2.

_M_e_t_h_o_d_s:


     _a_t_t_a_c_h_E_x_p_r 'signature(object = "ExprTreeSet")': exports expression
          trees from  'ROOT' expression file and and saves as
          data.frame 'data'.

     _e_x_p_r_T_y_p_e 'signature(object = "ExprTreeSet")': extracts slot
          'exprtype'.

     _e_x_p_r_T_y_p_e<- 'signature(object = "ExprTreeSet", value =
          "character")': replaces slot 'exprtype'.

     _e_x_p_r_s 'signature(object = "ExprTreeSet")': extracts the expression
          data.frame.

     _e_x_p_r_s<- 'signature(object = "ExprTreeSet", value = "data.frame")':
          replaces the expression data.frame.

     _m_v_a_p_l_o_t 'signature(x = "ExprTreeSet")': creates an MvA-plot.

     _n_o_r_m_T_y_p_e 'signature(object = "ExprTreeSet")': extracts slot
          'normtype'.

     _n_o_r_m_T_y_p_e<- 'signature(object = "ExprTreeSet", value =
          "character")': replaces slot 'normtype'.

     _r_e_m_o_v_e_E_x_p_r 'signature(object = "ExprTreeSet")': replaces
          data.frame 'data'  with an empty data.frame of dim(0,0).

     _s_e._e_x_p_r_s 'signature(object = "ExprTreeSet")': extracts the
          standard deviation data.frame.

     _x_p_s_N_o_r_m_a_l_i_z_e 'signature(object = "ExprTreeSet")': applies
          normalization methods.

     _x_p_s_P_r_e_F_i_l_t_e_r 'signature(object = "ExprTreeSet")': applies
          prefiltering methods.

     _x_p_s_U_n_i_F_i_l_t_e_r 'signature(object = "ExprTreeSet")': applies
          unifiltering methods.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     related classes 'DataTreeSet', 'CallTreeSet'.

_E_x_a_m_p_l_e_s:

     showClass("ExprTreeSet")

