CallTreeSet-class            package:xps            R Documentation

_C_l_a_s_s _C_a_l_l_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' call 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 'mas5.call' or 'dabg.call',
     respectively.

_S_l_o_t_s:


     '_c_a_l_l_t_y_p_e': Object of class '"character"' representing the call
          type,  i.e. 'mas5' or 'dabg'.

     '_d_e_t_c_a_l_l': Object of class '"data.frame"'. The data.frame can
          contain  the detection calls stored in 'ROOT' call trees.

     '_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 (i.e. p-values) stored in 'ROOT' call 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' call trees are
          stored, usually 'CallTreeSet'.

     '_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' call 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_C_a_l_l 'signature(object = "CallTreeSet")': exports detection
          call data from  'ROOT' call file and and saves as data.frame
          'detcall'.

     _a_t_t_a_c_h_P_V_a_l 'signature(object = "CallTreeSet")': exports call
          p-values from  'ROOT' call file and and saves as data.frame
          'data'.

     _c_a_l_l_p_l_o_t 'signature(x = "CallTreeSet")': creates a barplot of
          percent present and absent calls.

     _p_r_e_s_C_a_l_l 'signature(object = "CallTreeSet")': extracts the
          detection call data.frame.

     _p_r_e_s_C_a_l_l<- 'signature(object = "CallTreeSet", value =
          "data.frame")': replaces the detection call data.frame.

     _p_v_a_l_D_a_t_a 'signature(object = "CallTreeSet")': extracts the
          detection p-value data.frame.

     _p_v_a_l_D_a_t_a<- 'signature(object = "CallTreeSet", value =
          "data.frame")': replaces the detection p-value data.frame.

     _r_e_m_o_v_e_C_a_l_l 'signature(object = "CallTreeSet")': replaces
          data.frame 'detcall'  with an empty data.frame of dim(0,0).

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

     _v_a_l_i_d_C_a_l_l 'signature(object = "CallTreeSet")': extracts a subset
          of columns  from data.frame 'detcall'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     related classes 'DataTreeSet', 'ExprTreeSet'.

_E_x_a_m_p_l_e_s:

     showClass("CallTreeSet")

