ExpressionSetList-class         package:XDE         R Documentation

_A _c_l_a_s_s _f_o_r _c_o_n_t_a_i_n_i_n_g _a _l_i_s_t _o_f _E_x_p_r_e_s_s_i_o_n_S_e_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Each element in the list must be a valid 'ExpressionSet'.  The
     'featureNames' must be identical for each 'ExpressionSet'.

_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("ExpressionSetList", ...)'.

_S_l_o_t_s:


     '._D_a_t_a': Object of class '"list"'

_E_x_t_e_n_d_s:

     Class '"list"', from data part. Class '"vector"', by class "list",
     distance 2. Class 'class.AssayData', by class "list", distance 2.

_M_e_t_h_o_d_s:



     ._i_n_t_e_g_r_a_t_i_v_e_C_o_r_r_e_l_a_t_i_o_n_F_i_l_t_e_r 'signature(object =
          "ExpressionSetList")' Experimental function for filtering an
          arbitrary list of ExpressionSets by integrative correlation. 
          Genes are excluded that do not exceed the fdr threshold in at
          least 1 of the studies.

     "[" 'signature(x = "ExpressionSetList")' Subsets each
          'ExpressionSet' element in the list.

     _c_o_e_r_c_e 'signature(from = "list", to = "ExpressionSetList")'
          Coerces a list of 'ExpressionSet' objects to an object of
          class 'ExpressionSetList'. The 'validityMethod' for the
          'ExpressionSetList' class will return an error if the
          'featureNames' for each 'ExpressionSet' are not identical.

     _f_e_a_t_u_r_e_N_a_m_e_s 'signature(object = "ExpressionSetList")' Accessor
          for the 'featureNames'

     _g_e_n_e_C_e_n_t_e_r 'signature(object = "ExpressionSetList")' See
          'geneCenter'

     _l_a_p_p_l_y 'signature(object="ExpresssionSetList")' Coerces instance
          of ExpressionSetList to a list and does lapply on the list.
          Returns an object of class ExpressionSetList

     _n_S_a_m_p_l_e_s 'signature(x = "ExpressionSetList")' Numerical vector
          giving the number of samples in each 'ExpressionSet'

     _n_r_o_w 'signature(x = "ExpressionSetList")' Numerical: number of
          features or genes

     _p_D_a_t_a 'signature(object = "ExpressionSetList")' returns a list of
          'data.frames'.  The elements of the list correspond to the
          studies in the 'ExpressionSetList' object.

     ._p_c_a 'signature(object = "ExpressionSetList")' Runs principal
          components to generate cross-study summary scores of
          differential expression in multiple studies.  Not meant to be
          called directly.  See 'xsScores'.

     _s_t_a_n_d_a_r_d_i_z_e_S_a_m_p_l_e_s 'signature(object = "ExpressionSetList")' See
          'standardizeSamples'


     _s_t_u_d_y_C_e_n_t_e_r 'signature(object = "ExpressionSetList")' See
          'studyCenter'


     _x_a_p_p_l_y 'signature(object="ExpressionSetList")' An lapply for
          'ExpressionSetList' instances.  See 'xapply'.

     _z_e_r_o_N_u 'signature(object = "ExpressionSetList")' See '`zeroNu'. 

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     'XdeMcmc-class', 'XdeParameter-class'

_E_x_a_m_p_l_e_s:

     showClass("ExpressionSetList")
     data(expressionSetList)

