SchemeTreeSet-class           package:xps           R Documentation

_C_l_a_s_s _S_c_h_e_m_e_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' scheme file and  the
     'ROOT' trees contained therein. It extends class 'TreeSet'.

_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.expr.scheme',
     'import.exon.scheme', 'import.genome.scheme' or 'root.scheme'.

_S_l_o_t_s:


     '_c_h_i_p_n_a_m_e': Object of class '"character"' representing the
          Affymetrix chip name.

     '_c_h_i_p_t_y_p_e': Object of class '"character"' representing the chip
          tpye,  either 'GeneChip', 'GenomeChip' or 'ExonChip'.

     '_p_r_o_b_e_i_n_f_o': Object of class '"list"' representing chip
          information,  including nrows, ncols, number of probes, etc.

     '_m_a_s_k': Object of class '"data.frame"'. The data.frame can contain
          the mask  used to identify the probes as e.g. PM, MM or
          control probes.

     '_s_e_t_n_a_m_e': Object of class '"character"' representing the name to
          the 'ROOT' file subdirectoy where the 'ROOT' scheme trees are
          stored; it is identical to 'chipname'.

     '_s_e_t_t_y_p_e': Object of class '"character"' describing the type of
          treeset stored in 'setname', i.e. 'scheme'.

     '_r_o_o_t_f_i_l_e': Object of class '"character"' representing the name 
          of the 'ROOT' scheme 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 '"TreeSet"', directly.

_M_e_t_h_o_d_s:


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

     _c_h_i_p_M_a_s_k 'signature(object = "SchemeTreeSet")': extracts
          data.frame 'mask'.

     _c_h_i_p_M_a_s_k<- 'signature(object = "SchemeTreeSet", value =
          "data.frame")': replaces  data.frame 'mask'.

     _c_h_i_p_N_a_m_e 'signature(object = "SchemeTreeSet")': extracts slot
          'chipname'.

     _c_h_i_p_T_y_p_e 'signature(object = "SchemeTreeSet")': extracts slot
          'chiptype'.

     _c_h_i_p_T_y_p_e<- 'signature(object = "SchemeTreeSet", value =
          "character")': replaces  slot 'chiptype'.

     _e_x_p_o_r_t 'signature(object = "SchemeTreeSet")': exports 'ROOT' trees
           as text file, see 'export-methods'.

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

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

     _p_r_o_b_e_I_n_f_o 'signature(object = "SchemeTreeSet")': extracts slot
          'probeinfo'.

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

_A_u_t_h_o_r(_s):

     Christian Stratowa

_E_x_a_m_p_l_e_s:

     showClass("SchemeTreeSet")

