eSet-class              package:Biobase              R Documentation

_C_l_a_s_s "_e_S_e_t": _a _n_e_w _e_x_p_r_S_e_t _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     A second attempt at a universal definition of experimental data,
     combined with phenotypic data and in some cases probe data.

_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("eSet", ...)'.
     These objects are basically structured to provide a unified and
     simplified set of methods for handling experimental data. This
     might be gene expression data, array CGH data or
     SELD-TOF/MALDI-TOF data.

_S_l_o_t_s:

     '_e_L_i_s_t': Object of class '"exprList"' containing the experimental
          data. 

     '_p_h_e_n_o_D_a_t_a': Object of class '"phenoData"' containing the
          phenotypic or sample level data.

_M_e_t_h_o_d_s:

     [ 'signature(x = "eSet")': basic subsetting. It returns an object
          of class 'eSet'. The first index subsets experimental units
          while the second subsets samples. 

     _c_o_m_b_i_n_e 'signature(x = "eSet", y = "eSet")': a method for merging
          two 'eSet's. Substantial checking is carried out. 

     _c_o_m_b_i_n_e 'signature(x = "eSet", y = "ANY")': As above. 

     _e_L_i_s_t 'signature(object = "eSet")': a container for the
          experimental data. This can accomodate multiple channels etc. 

     _e_L_i_s_t<- 'signature(object = "eSet", value = "exprList")': An
          assignment function for 'exprList's. 

     _e_L_i_s_t<- 'signature(object = "eSet", value = "environment")': as
          above

     _e_L_i_s_t<- 'signature(object = "eSet", value = "list")': as above.

     _e_x_p_r_s 'signature(object = "eSet")': extract the experimental data. 

     _g_e_t_E_x_p_D_a_t_a 'signature(object = "eSet", name = "character")':
          extract the experimental data.

     _p_D_a_t_a 'signature(object = "eSet")': get the actual 'data.frame'
          containing the phenotypic data. 

     _p_D_a_t_a<- 'signature(object = "eSet")': replace the actual
          'data.frame' containing the phenotypic data.

     _p_h_e_n_o_D_a_t_a 'signature(object = "eSet")': extract the phenoData
          object (data frame plus descriptions of the covariates). 

     _p_h_e_n_o_D_a_t_a<- 'signature(object = "eSet", value = "phenoData")': a
          replacement method for the 'phenoData' object. 

     _s_h_o_w 'signature(object = "eSet")': a print method, to control
          printing vast amounts of data. 

_N_o_t_e:

     The data structures etc. were designed by a consensus view of
     Biocore.

_A_u_t_h_o_r(_s):

     Biocore

_S_e_e _A_l_s_o:

     'exprSet-class'

_E_x_a_m_p_l_e_s:

     ##---- Should be DIRECTLY executable !! ----

