stamLeaf-class             package:stam             R Documentation

_L_e_a_f _N_o_d_e_s _i_n _C_l_a_s_s_i_f_i_e_r _N_e_t_s _b_y _S_t_A_M

_D_e_s_c_r_i_p_t_i_o_n:

     Objects of this class represent leaf nodes in a classifier net as
     it is used by structured analysis of microarray data. These are
     the only nodes which have genes  annotated.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form  'new("stamLeaf", ID,
     chip, probesidx)'.

     '_I_D' is the GO identifier as character string

     '_c_h_i_p' the name of the chip for which the classifier net is
          generated.

     '_p_r_o_b_e_s' a character vector holding the identifiers of the
          probesets in  the order as they occur in the expression
          matrix

_S_l_o_t_s:


     '_c_h_i_p': Object of class '"character"', the name of the chip for 
          which the classifier net is generated.

     '_p_r_o_b_e_s': Object of class '"numeric"', for each probeset holds its
           position in the expression metrices to be analyzed 

     '_p_a_m_f_i_t': Object of class '"nsc"', holds the results of pamr.train
           restricted to the genes annotated to the current leaf node.

     '_d_e_l_t_a': Object of class '"numeric"', stores the best delty for
          the  local pamfit as determined by pamr.cv.

     See 'stamNode-class' fot 'ID', 'category', 'replacedParents' and 
     'supNode'.

_E_x_t_e_n_d_s:

     Class '"stamNode"', directly.

_M_e_t_h_o_d_s:


     _p_r_i_n_t 'signature(x = "stamLeaf")': print information on the leaf
          node.

     _w_r_i_t_e_H_T_M_L 'signature(x = "stamLeaf")': generate HTML information
          on the  leaf node.

_A_u_t_h_o_r(_s):

     Claudio Lottaz

_S_e_e _A_l_s_o:

     'stamNode-class', 'stamINode-class'

