QCIllumina-class        package:beadarraySNP        R Documentation

_C_l_a_s_s "_Q_C_I_l_l_u_m_i_n_a"

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

     Container of QC information on arrays that contain multiple
     samples.

_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("QCIllumina",
     arrayType, arrayID,  intensityMed, greenMed, redMed,
     intensityMode, greenMode, redMode, validn, annotation,  samples)',
     but are usually created by 'calculateQCarray'.

_S_l_o_t_s:


     '_a_r_r_a_y_T_y_p_e': character, Type of array. See  'arrayType' 

     '_a_r_r_a_y_I_D': character, Array ID 

     '_i_n_t_e_n_s_i_t_y_M_e_d': numeric matrix, Median of intensity of samples 

     '_g_r_e_e_n_M_e_d': numeric matrix, Median of green values 

     '_r_e_d_M_e_d': numeric matrix, Median of red values 

     '_v_a_l_i_d_n': numeric matrix, Number of valid probe values in samples 

     '_a_n_n_o_t_a_t_i_o_n': character matrix, Annotation of samples 

     '_s_a_m_p_l_e_s': character matrix, Sample IDs 

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


     _a_r_r_a_y_I_D 'signature(object = "QCIllumina")': Returns type of array 

     _a_r_r_a_y_I_D<- 'signature(object = "QCIllumina")': Sets type of array. 
          Currently only '"Sentrix"' is supported 

     _a_r_r_a_y_T_y_p_e 'signature(object = "QCIllumina")': Returns ID of array 

     _a_r_r_a_y_T_y_p_e<- 'signature(object = "QCIllumina")': Sets ID/Barcode of
          array 

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

     _p_l_o_t_Q_C 'signature(object = "QCIllumina")''character': plots
          spatial overview of QC information, 'type' is one of
          'c("intensityMed",
          "greenMed","redMed","validn","annotation","samples")'   

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

     Jan Oosting

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

     'calculateQCarray'

