beadData-class         package:BeadExplorer         R Documentation

_C_l_a_s_s "_b_e_a_d_D_a_t_a"

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

     A class to hold data information from a BeadChip 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("beadData",
     ...)'.

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

     '_f_i_l_e_O_r_i_g_i_n': Object of class '"character"': File paths of the
          data used to create the object 

     '_p_a_r_a_m': Object of class '"list"': Parameters extracted from the
          source files 

     '_n_o_r_m_M_e_t_h_o_d': Object of class '"character"': The normalisation
          method applied to the object (if any) 

     '_d_e_t_E_x_p_r_s': Object of class '"matrix"': BeadStudio detection
          scores 

     '_e_x_p_r_s': Object of class '"exprMatrix"': Unlogged intensity data 

     '_s_e._e_x_p_r_s': Object of class '"exprMatrix"': Standard errors of
          bead replicates  

     '_d_e_s_c_r_i_p_t_i_o_n': Object of class '"character OR MIAME"'  

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"': A name given to the
          analysis

     '_n_o_t_e_s': Object of class '"character"': Notes 

     '_r_e_p_o_r_t_e_r_I_n_f_o': Object of class '"data.frame Or NULL"': reporter
          info

     '_p_h_e_n_o_D_a_t_a': Object of class '"phenoData"': Phenotype data

_E_x_t_e_n_d_s:

     Class '"exprSet"', directly. Class '"annotatedDataset"', by class
     '"exprSet"'.

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

     [ 'signature(x = "beadData")': subset for samples

     _b_o_x_p_l_o_t 'signature(x = "beadData")': boxplot of expression data

     _d_e_t_e_c_t_i_o_n_C_a_l_l_s 'signature(object = "beadData")': Obtain detection
          calls  

     _d_e_t_E_x_p_r_s 'signature(object = "beadData")': slot accessor method 

     _f_i_l_e_O_r_i_g_i_n 'signature(object = "beadData")': slot accessor method 

     _n_G_e_n_e_s 'signature(object = "beadData")': Number of transcripts 

     _n_o_r_m_M_e_t_h_o_d 'signature(object = "beadData")': slot accessor method

     _n_S_a_m_p_l_e_s 'signature(object = "beadData")': Number of samples 

     _p_a_i_r_s 'signature(x = "beadData")': Plot pairwise intensity plots 

     _p_a_r_a_m 'signature(object = "beadData")': slot accessor method 

     _s_i_g_n_a_l_M_e_a_n_s 'signature(object = "beadData")': Obtain signal means 

     _s_u_m_m_a_r_y 'signature(object = "beadData")': Obtain summary of the
          data 

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

     Gareth Elvidge gareth.elvidge@well.ox.ac.uk

_E_x_a_m_p_l_e_s:

     data(examplebeadData)
     nGenes(examplebeadData)

