MultiSet               package:Biobase               R Documentation

_C_l_a_s_s _t_o _C_o_n_t_a_i_n _a_n_d _D_e_s_c_r_i_b_e _H_i_g_h-_T_h_r_o_u_g_h_p_u_t _E_x_p_r_e_s_s_i_o_n _L_e_v_e_l _A_s_s_a_y_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Container for high-throughput assays and experimental metadata.
     'MutliSet' is derived from 'eSet-class'. 'MultiSet' differs from
     'ExpressionSet-class' because 'MultiSet' can contain any
     element(s) in 'assayData' ('ExpressionSet' must have an element
     named 'exprs').

_E_x_t_e_n_d_s:

     Directly extends class 'eSet'.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     'new('MultiSet', phenoData = [AnnotatedDataFrame], experimentData
     = [MIAME], annotation = [character], ...) '

     'updateOldESet(oldESet,"MultiSet")'

     'MultiSet' instances are usually created through 'new("MultiSet",
     ...)'. The '...' arguments to 'new' are matrices of expression
     data (with features corresponding to rows and samples to columns),
     'phenoData', 'experimentData', and 'annotation'.  'phenoData',
     'experimentData', and 'annotation' can be missing, in which case
     they are assigned default values.

     'updateOldESet' will take a serialized instance (e.g., saved to a
     disk file with 'save' object created with earlier definitions of
     the 'eSet-class', and update the object to 'MultiSet'. Warnings
     are issued when direct translation is not possible; incorrectly
     created 'oldESet' instances may not be updated.

_S_l_o_t_s:

     Inherited from 'eSet':

     '_a_s_s_a_y_D_a_t_a': Contains zero or more matrices with equal dimensions,
          and with column number equal to 'nrow(phenoData)'. Each
          matrix in 'assayData' has rows represening features (e.g.,
          reporters) and columns representing samples.
          Class:'AssayData-class'

     '_p_h_e_n_o_D_a_t_a': See 'eSet-class'

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': See 'eSet-class'

     '_a_n_n_o_t_a_t_i_o_n': See 'eSet-class'

_M_e_t_h_o_d_s:

     Class-specific methods: none

     Derived from 'eSet-class':

     '_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' and 'eSet'

     '_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'

     '_s_a_m_p_l_e_N_a_m_e_s(_M_u_l_t_i_S_e_t)' _a_n_d '_s_a_m_p_l_e_N_a_m_e_s(_M_u_l_t_i_S_e_t)<-': See
          'eSet-class'

     '_f_e_a_t_u_r_e_N_a_m_e_s(_M_u_l_t_i_S_e_t)', '_f_e_a_t_u_r_e_N_a_m_e_s(_M_u_l_t_i_S_e_t, _v_a_l_u_e)<-': See
          'eSet-class'

     '_d_i_m_s(_M_u_l_t_i_S_e_t)': See 'eSet-class'

     '_p_h_e_n_o_D_a_t_a(_M_u_l_t_i_S_e_t)', '_p_h_e_n_o_D_a_t_a(_M_u_l_t_i_S_e_t,_v_a_l_u_e)<-': See
          'eSet-class'

     '_v_a_r_L_a_b_e_l_s(_M_u_l_t_i_S_e_t)', '_v_a_r_L_a_b_e_l_s(_M_u_l_t_i_S_e_t, _v_a_l_u_e)<-': See
          'eSet-class'

     '_v_a_r_M_e_t_a_d_a_t_a(_M_u_l_t_i_S_e_t)', '_v_a_r_M_e_t_a_d_a_t_a(_M_u_l_t_i_S_e_t,_v_a_l_u_e)<-': See
          'eSet-class'

     '_p_D_a_t_a(_M_u_l_t_i_S_e_t)', '_p_D_a_t_a(_M_u_l_t_i_S_e_t,_v_a_l_u_e)<-': See 'eSet-class'

     '_v_a_r_M_e_t_a_d_a_t_a(_M_u_l_t_i_S_e_t)', '_v_a_r_M_e_t_a_d_a_t_a(_M_u_l_t_i_S_e_t,_v_a_l_u_e)' See
          'eSet-class'

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a(_M_u_l_t_i_S_e_t)','_e_x_p_e_r_i_m_e_n_t_D_a_t_a(_M_u_l_t_i_S_e_t,_v_a_l_u_e)<-': See
          'eSet-class'

     '_p_u_b_M_e_d_I_d_s(_M_u_l_t_i_S_e_t)', '_p_u_b_M_e_d_I_d_s(_M_u_l_t_i_S_e_t,_v_a_l_u_e)' See
          'eSet-class'

     '_a_b_s_t_r_a_c_t(_M_u_l_t_i_S_e_t)': See 'eSet-class'

     '_a_n_n_o_t_a_t_i_o_n(_M_u_l_t_i_S_e_t)', '_a_n_n_o_t_a_t_i_o_n(_M_u_l_t_i_S_e_t,_v_a_l_u_e)<-' See
          'eSet-class'

     '_c_o_m_b_i_n_e(_M_u_l_t_i_S_e_t,_M_u_l_t_i_S_e_t)': See 'eSet-class'

     '_s_t_o_r_a_g_e_M_o_d_e(_e_S_e_t)', '_s_t_o_r_a_g_e_M_o_d_e(_e_S_e_t,_c_h_a_r_a_c_t_e_r)<-': See
          'eSet-class'

     '_r_e_p_o_r_t_e_r_N_a_m_e_s(_M_u_l_t_i_S_e_t)', '_r_e_p_o_r_t_e_r_N_a_m_e_s(_M_u_l_t_i_S_e_t,_v_a_l_u_e)<-': DEPR
          ECATED

     Standard generic methods:

     '_i_n_i_t_i_a_l_i_z_e(_M_u_l_t_i_S_e_t)': Object instantiation, used by 'new'; not
          to be called directly by the user.

     '_v_a_l_i_d_O_b_j_e_c_t(_M_u_l_t_i_S_e_t)': Validity-checking method, ensuring that
          all elements of 'assayData' are matricies with equal
          dimensions.

     '_a_s(_e_S_e_t,_M_u_l_t_i_S_e_t)': Coerce the 'eSet' portion of an object to
          'MultiSet'.

     '_s_h_o_w(_M_u_l_t_i_S_e_t)' See 'eSet-class'

     '_d_i_m(_M_u_l_t_i_S_e_t)', '_n_c_o_l' See 'eSet-class'

     '_M_u_l_t_i_S_e_t[(_i_n_d_e_x)': See 'eSet-class'

     '_M_u_l_t_i_S_e_t$', '_M_u_l_t_i_S_e_t$<-' See 'eSet-class'

_A_u_t_h_o_r(_s):

     Biocore team

_S_e_e _A_l_s_o:

     'eSet-class', 'ExpressionSet-class'

_E_x_a_m_p_l_e_s:

     # create an instance of ExpressionSet
     new("MultiSet")

     # update existing eSet class to MultiSet
     data(sample.eSet)
     multiSet <- as(sample.eSet,"MultiSet")
     multiSet

     # information about assay and sample data
     featureNames(multiSet)[1:10]
     sampleNames(multiSet)[1:5]
     phenoData(multiSet)
     experimentData(multiSet)