BeadLevelList-class        package:beadarray        R Documentation

_C_l_a_s_s "_B_e_a_d_L_e_v_e_l_L_i_s_t"

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

     A class for storing red and green channel foreground and
     background intensities from an Illumina experiment.

_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("BeadLevelList")', but are usually created by 'readIllumina'.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     Objects of this class contain the following slots

       'beadData':     an environment for storing the raw  bead-level data.   Each row correspond to a bead and columns the data.
       'phenoData':    an 'AnnotatedDataFrame' containing   experimental information.
       'arrayInfo':    a list containing array information.
       'annotation':   character storing annotation package  information.
       'beadAnno':     a data.frame containing Bead annotation information.
       'scanMetrics':  a data.frame containing scanner information.

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

     _s_h_o_w(_B_e_a_d_L_e_v_e_l_L_i_s_t) printing method for BeadLevelList

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "BeadLevelList")'

     _d_i_m 'dim(object)'The dimension of the  'BeadLevelList' object

     '_c_o_p_y_B_e_a_d_L_e_v_e_l_L_i_s_t(_o_b_j_e_c_t)' Creates a new copy of a
          'BeadLevelList' object

     '_a_r_r_a_y_N_a_m_e_s(_o_b_j_e_c_t,_a_r_r_a_y_s=_N_U_L_L)' Returns the array names from a
          'BeadLevelList' object for selected 'arrays'

     '_c_o_m_b_i_n_e_B_e_a_d_L_e_v_e_l_L_i_s_t_s(_o_b_j_e_c_t_1,_o_b_j_e_c_t_2)' Combines two
          'BeadLevelList' objects into one

     '_g_e_t_A_r_r_a_y_D_a_t_a(_o_b_j_e_c_t,_w_h_a_t="_G",_l_o_g=_T_R_U_E)' Retrieves  the 'what'
          intensities on the 'log' scale from the 'BeadLevelList'

     '_n_u_m_B_e_a_d_s(_o_b_j_e_c_t,_a_r_r_a_y_s=_N_U_L_L)' Returns the number of beads on
          selected 'arrays'

     '_p_D_a_t_a(_o_b_j_e_c_t)' Returns a data.frame with samples as rows,
          variables as columns

     '_p_h_e_n_o_D_a_t_a(_o_b_j_e_c_t)' Returns an object containing phenotypic
          information on both variable values and variable meta-data

_A_u_t_h_o_r(_s):

     Mark Dunning

_S_e_e _A_l_s_o:

     'readIllumina'

