AssayData-class           package:Biobase           R Documentation

_C_l_a_s_s "_A_s_s_a_y_D_a_t_a"

_D_e_s_c_r_i_p_t_i_o_n:

     Container class defined as a class union of 'list' and
     'environment'.  Designed to contain one or more matrices of the
     same dimension.

_M_e_t_h_o_d_s:

     _a_s_s_a_y_D_a_t_a<- 'signature(object = "eSet", value = "AssayData")':
          Replace the 'AssayData' slot of a 'eSet' instance.

     _c_o_m_b_i_n_e 'signature(x = "AssayData", y = "AssayData")': Return a
          new AssayData instance with corresponding elements combined
          using 'cbind'.

     _f_e_a_t_u_r_e_N_a_m_e_s 'signature(object = "AssayData")'

     _f_e_a_t_u_r_e_N_a_m_e_s<- 'signature(object = "AssayData", value = "ANY")':
          Return or set the feature names as a character vector.  These
          are the row names of the AssayData elements. 'value' can be a
          character or numeric vector; all entries must be unique.

     _s_a_m_p_l_e_N_a_m_e_s 'signature(object = "AssayData")'

     _s_a_m_p_l_e_N_a_m_e_s<- 'signature(object = "AssayData", value="ANY")':
          Return or set the sample names.  These are the column names
          of the the AssayData elements and the row names of
          'phenoData'. 'value' can be a character or numeric vector.

     _s_t_o_r_a_g_e_M_o_d_e 'signature(object = "AssayData")'

     _s_t_o_r_a_g_e_M_o_d_e<- 'signature(object = "AssayData",
          value="character")': Return or set the storage mode for the
          instance. 'value' can be one of three choices:
          '"lockedEnvironment"', '"environment"', and '"list"'.
          Environments offer a mechanism for storing data that avoids
          some of the copying that occurs when using lists.  Locked
          environment help to ensure data integrity.  Note that
          environments are one of the few R objects that are
          pass-by-reference.  This means that if you modify a copy of
          an environment, you also modify the original. For this
          reason, we recommend using lockedEnvironment whenever
          possible.

     Additional functions operating on 'AssayData' include:

     _a_s_s_a_y_D_a_t_a_N_e_w(_s_t_o_r_a_g_e._m_o_d_e = _c("_l_o_c_k_e_d_E_n_v_i_r_o_n_m_e_n_t", "_e_n_v_i_r_o_n_m_e_n_t", "_l_i_s_t"), ...) Use
          'storage.mode' to create a new list or environment containing
          the named elements in '...'

     _a_s_s_a_y_D_a_t_a_V_a_l_i_d_M_e_m_b_e_r_s(_a_s_s_a_y_D_a_t_a, _r_e_q_u_i_r_e_d) Validate 'assayData',
          ensuring that the named elements 'required' are present,
          matrices are of the same dimension, and 'featureNames'
          (rownames) are consistent (identical or 'NULL') across
          entries.

     _a_s_s_a_y_D_a_t_a_E_l_e_m_e_n_t(_o_b_j_e_c_t, _e_l_e_m_e_n_t) See 'eSet-class'

     _a_s_s_a_y_D_a_t_a_E_l_e_m_e_n_t_R_e_p_l_a_c_e(_o_b_j_e_c_t, _e_l_e_m_e_n_t, _v_a_l_u_e) See 'eSet-class'

     _a_s_s_a_y_D_a_t_a_E_l_e_m_e_n_t_N_a_m_e_s(_o_b_j_e_c_t) See 'eSet-class'

_A_u_t_h_o_r(_s):

     Biocore

_S_e_e _A_l_s_o:

     'eSet-class' 'ExpressionSet-class'