phenoData-class           package:Biobase           R Documentation

_C_l_a_s_s _p_h_e_n_o_D_a_t_a, _a _c_l_a_s_s _f_o_r _p_a_t_i_e_n_t _o_r _e_x_p_e_r_i_m_e_n_t _l_e_v_e_l _d_a_t_a.

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

     The class consists of a 'data.frame' and some accompanying methods
     suited to handle patient level data for microarrays.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     '  new('phenoData','
      '    pData     = ...., # Object of class \code{data.frame}'
      '    varLabels = ...., # Object of class \code{list}'
      '    varMetadata = ...., # Object of class \code{data.frame}'
      '  )'

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

     '_p_D_a_t_a': Object of class "data.frame". The data. 

     '_v_a_r_L_a_b_e_l_s': Object of class "list". Obtional long labels for the
          different variables. 

     '_v_a_r_M_e_t_a_d_a_t_a': Object of class "data.frame". A data frame with a
          column named varNames and arbitrarily many additional
          columns. 

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

     [ (phenoData): A subset operator. 

     _p_D_a_t_a (phenoData): An accessor function for 'pData'.

     _s_h_o_w (phenoData): A method to display the data in a nice manner. 

     _v_a_r_L_a_b_e_l_s (phenoData): A method to display the variable labels. 

     _s_p_l_i_t (phenoData, vector): A method to 'split' 'pData' and return
          a list of 'phenoData' objects. Unlike 'split' this function
          requires the number of rows of 'pData' to be a multiple of
          the length of 'vector'.

     $ An old-style method. It is 'pData(object)[[as.character(val)]]'
          which does not quite have the right semantics but it is
          close. This operator extracts the named component of the
          'pData' slot in 'phenoData'.

     _p_D_a_t_a<- (phenoData): A replacement method for the 'pData' slot.

     _p_h_e_n_o_D_a_t_a<- (exprSet): A replacement method for the 'phenoData'
          slot.

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

     data(eset)
     pes <- phenoData(eset)
     pes <- convertVarLabels(pes)
     varMetadata(pes)
     pes <- addVarMetadataEntry(pes, "cov1", "units", "inches")
     getUnits(pes, "cov1")

