phenoData              package:Biobase              R Documentation

_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 = [data.frame], varLabels = [list],
     varMetadata = [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:

     Class-specific methods:

     '_c_o_m_b_i_n_e(_p_h_e_n_o_D_a_t_a, _p_h_e_n_o_D_a_t_a)' Combines several instances into a
          single 'phenoData' instance. See 'combine'

     '_c_o_n_v_e_r_t_V_a_r_L_a_b_e_l_s(_p_h_e_n_o_D_a_t_a)' Not documented

     '_g_e_t_V_a_r_M_e_t_a_d_a_t_a(_p_h_e_n_o_D_a_t_a, _c_h_a_r_a_c_t_e_r, _c_h_a_r_a_c_t_e_r)' _o_r '_g_e_t_V_a_r_M_e_t_a_d_a_t_a(_p_h_e_n_o_D_a_t_a, _c_h_a_r_a_c_t_e_r, _m_i_s_s_i_n_g)' Not
          documented

     '_p_D_a_t_a(_p_h_e_n_o_D_a_t_a), _p_D_a_t_a(_p_h_e_n_o_D_a_t_a)<-' Get/set methods for slot
          'pData'

     '_p_h_e_n_o_D_a_t_a(_e_x_p_r_S_e_t)<-' A replacement method for the 'phenoData'
          slot

     '_s_p_l_i_t(_p_h_e_n_o_D_a_t_a, _v_e_c_t_o_r)' FIXME: there is no implementation!!! 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'

     '_v_a_r_L_a_b_e_l_s(_p_h_e_n_o_D_a_t_a)' A method to display the variable labels. 

     '_v_a_r_M_e_t_a_d_a_t_a(_p_h_e_n_o_D_a_t_a)' Not documented

     Standard methods defined for 'phenoData':

     '$(_n_a_m_e), $(_n_a_m_e, _v_a_l_u_e)<-' An old-style method to get and set. 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_h_e_n_o_D_a_t_a)' A subset operator

     '[[(_p_h_e_n_o_D_a_t_a), [[(_p_h_e_n_o_D_a_t_a)<-' A get/set subset operator

     '_s_h_o_w(_p_h_e_n_o_D_a_t_a)' Displays the data in a readable manner

     Functions defined in Biobase to operate with 'phenoData' instances
     include:

     '_u_p_d_a_t_e_O_b_j_e_c_t(_o_b_j_e_c_t, ..., _v_e_r_b_o_s_e=_F_A_L_S_E)' Update instance to
          current version, if necessary. See 'updateObject'

     '_i_s_C_u_r_r_e_n_t(_o_b_j_e_c_t)' Determine whether version of object is
          current. See 'isCurrent'

     '_i_s_V_e_r_s_i_o_n_e_d(_o_b_j_e_c_t)' Determine whether object contains a
          'version' string describing its structure . See 'isVersioned'

     '_d_f_2_p_D(_x, _v_a_r_L_a_b_e_l_s, _v_a_r_M_e_t_a_d_a_t_a)' Function to coerce from a
          'data.frame' to a 'phenoData' object. Here 'x' is the
          'data.frame' to be coerced; 'varLabels' is a character
          describing each of the columns in 'x' and 'varMetadata' is a
          more extensive descriptions of the variables in 'x',
          including units of measurement etc

     '_r_e_a_d._p_h_e_n_o_D_a_t_a' See help on 'read.phenoData'

_S_e_e _A_l_s_o:

     'read.phenoData', 'combine'

_E_x_a_m_p_l_e_s:

     data(sample.exprSet)
     pes <- phenoData(sample.exprSet)
     pes <- convertVarLabels(pes)
     varMetadata(pes)

     # example for 'df2pD'
     data(cars)
     d1 = df2pD(cars)

     # update phenoData to current class description
     updateObject(phenoData(sample.exprSet))