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 simple list-based class for storing red and green channel
     foreground and background intensities for 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",
     G, Gb, x, y, ProbeID, targets)', but are usually created by
     'readBeadLevelData'.

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

     'BeadLevelList' objects can be created by
     'new("BeadLevelList",BLData)' where 'BLData' is a list. Objects of
     this class contains no slots (other than '.Data'), but objects
     should contain the following list components:

       'R':   numeric matrix containing the red (foreground intensities.  Rows correspond to spots and columns to arrays.
       'G':   numeric matrix containing the green foreground intensities
       'Rb':  numeric matrix containing the red  background intensities
       'Gb':  numeric matrix containing the green background intensities

_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")'  

     _c_r_e_a_t_e_B_e_a_d_S_u_m_m_a_r_y_D_a_t_a Summarise each probe on the array to create
          an 'ExpressionSetIlluminaObject'

     '_i_m_a_g_e_p_l_o_t(_B_e_a_d_L_e_v_e_l_L_i_s_t)' An imageplot function for
          'BeadLevelList'

     '_f_i_n_d_A_l_l_O_u_t_l_i_e_r_s(_B_e_a_d_L_e_v_e_l_L_i_s_t)' Find all beads on an array that
          are outliers for their particular bead type

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

     Mark Dunning

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

     'readBeadLevelData'

