DataTreeSet-class            package:xps            R Documentation

_C_l_a_s_s _D_a_t_a_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' data 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 can be created using the functions 'import.data' or
     'root.data'.

_S_l_o_t_s:


     '_b_g_t_r_e_e_n_a_m_e_s': Object of class '"list"' representing the names of 
           optional 'ROOT' background trees.

     '_b_g_r_d': Object of class '"data.frame"'. The data.frame can contain
           background intensities stored in 'ROOT' background trees.

     '_p_r_o_j_e_c_t_i_n_f_o': Object of class '"ProjectInfo"' containing
          information  about the project.

     '_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. intensities) 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 'DataTreeSet'.

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

     '_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_d_d_D_a_t_a 'signature(object = "DataTreeSet")': import additional
          CEL-files and  update 'ROOT' data file 'rootfile'.

     _a_t_t_a_c_h_B_g_r_d 'signature(object = "DataTreeSet")': exports background
          trees from  'ROOT' data file and and saves as data.frame
          'bgrd'.

     _a_t_t_a_c_h_I_n_t_e_n 'signature(object = "DataTreeSet")': exports intensity
          trees from  'ROOT' data file and and saves as data.frame
          'data'.

     _a_t_t_a_c_h_M_a_s_k 'signature(object = "DataTreeSet")': exports scheme
          tree from  'ROOT' scheme file and and saves as data.frame
          'mask' of slot 'scheme'.

     _b_a_c_k_g_r_o_u_n_d 'signature(object = "DataTreeSet")': extracts slot
          'bgrd'.

     _b_a_c_k_g_r_o_u_n_d<- 'signature(object = "DataTreeSet", value =
          "data.frame")': replaces slot 'bgrd'.

     _b_g_t_r_e_e_N_a_m_e_s 'signature(object = "DataTreeSet")': extracts slot
          'bgtreenames'.

     _i_m_a_g_e 'signature(x = "DataTreeSet")': creates an image for each
          column from data.frame 'data' or  'bgrd', respectively.

     _i_n_t_e_n_s_i_t_y 'signature(object = "DataTreeSet")': extracts slot
          'data'.

     _i_n_t_e_n_s_i_t_y<- 'signature(object = "DataTreeSet", value =
          "data.frame")': replaces slot 'data'.

     _m_m 'signature(object = "DataTreeSet")': extracts the mismatch
          intensities.

     _n_c_o_l_s 'signature(object = "DataTreeSet")': extracts the physical
          number of  array columns from slot 'scheme'.

     _n_r_o_w_s 'signature(object = "DataTreeSet")': extracts the physical
          number of  array rows from slot 'scheme'.

     _p_m 'signature(object = "DataTreeSet")': extracts the perfect match
          intensities.

     _p_m_p_l_o_t 'signature(x = "DataTreeSet")': creates a barplot of mean
          perfect match and mismatch intensities.

     _p_r_o_j_e_c_t_I_n_f_o 'signature(object = "DataTreeSet")': extracts slot
          'projectinfo'.

     _p_r_o_j_e_c_t_I_n_f_o<- 'signature(object = "DataTreeSet", value =
          "ProjectInfo")': replaces slot 'projectinfo'.

     _r_a_w_C_E_L_N_a_m_e 'signature(object = "DataTreeSet")': returns the
          name(s) of the  imported raw CEL-files.

     _r_e_m_o_v_e_B_g_r_d 'signature(object = "DataTreeSet")': replaces
          data.frame 'bgrd'  with an empty data.frame of dim(0,0).

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

     _r_e_m_o_v_e_M_a_s_k 'signature(object = "DataTreeSet")': replaces
          data.frame 'mask'  from slot 'scheme' with an empty
          data.frame of dim(0,0).

     _v_a_l_i_d_B_g_r_d 'signature(object = "DataTreeSet")': extracts the valid
          data  from data.frame 'bgrd'.

     _v_a_l_i_d_D_a_t_a 'signature(object = "DataTreeSet")': extracts a subset
          of valid data  from data.frame 'data'.

     _x_p_s_B_g_C_o_r_r_e_c_t 'signature(object = "DataTreeSet")': applies
          background correction methods. See 'bgcorrect'.

     _x_p_s_D_A_B_G_C_a_l_l 'signature(object = "DataTreeSet")': computes DABG
          call.

     _x_p_s_I_N_I_C_a_l_l 'signature(object = "DataTreeSet")': computes I/NI
          call.

     _x_p_s_M_A_S_4 'signature(object = "DataTreeSet")': computes MAS4
          expression levels.

     _x_p_s_M_A_S_5 'signature(object = "DataTreeSet")': computes MAS5
          expression levels.

     _x_p_s_M_A_S_5_C_a_l_l 'signature(object = "DataTreeSet")': computes MAS5
          detection call.

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

     _x_p_s_P_r_e_p_r_o_c_e_s_s 'signature(object = "DataTreeSet")': applies
          normalization methods.

     _x_p_s_R_M_A 'signature(object = "DataTreeSet")': computes RMA
          expression levels.

     _x_p_s_S_u_m_m_a_r_i_z_e 'signature(object = "DataTreeSet")': applies
          summarization methods.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     related classes 'ExprTreeSet', 'CallTreeSet'.

_E_x_a_m_p_l_e_s:

     showClass("DataTreeSet")

