SnpLevelSet-class        package:oligoClasses        R Documentation

_C_l_a_s_s "_S_n_p_L_e_v_e_l_S_e_t"

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

     Virtual class for SNP-level data

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     A virtual Class: No objects may be created from it.

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



     '_a_s_s_a_y_D_a_t_a': The usual restrictions on 'assayData': contains
          matrices with equal dimensions, and with column number equal
          to 'nrow(phenoData)'. Class:'class.AssayData'

     '_p_h_e_n_o_D_a_t_a': See 'class.eSet'

     '_f_e_a_t_u_r_e_D_a_t_a': See 'class.eSet'

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': See 'class.eSet'

     '_a_n_n_o_t_a_t_i_o_n': See 'class.eSet'

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class '"Versions"' 

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

     Class 'eSet', directly. Class 'VersionedBiobase', by class "eSet",
     distance 2. Class 'Versioned', by class "eSet", distance 3.

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


     _c_a_l_l_s 'signature(object = "SnpLevelSet")': Accessor for matrix of
          genotype calls

     _c_a_l_l_s<- 'signature(object = "SnpLevelSet", value = "matrix")':
          Replacement method for genotype calls.

     _c_a_l_l_s_C_o_n_f_i_d_e_n_c_e 'signature(object = "SnpLevelSet")': Accessor for
          matrix of confidence scores for the genotype calls

     _c_a_l_l_s_C_o_n_f_i_d_e_n_c_e<- 'signature(object = "SnpLevelSet", value =
          "matrix")': Replacement method

     _c_h_r_o_m_o_s_o_m_e 'signature(object = "SnpLevelSet")': See also
          'chromosome'

     _c_h_r_o_m_o_s_o_m_e<- 'signature(object = "SnpLevelSet", value =
          "character")': See also 'chromosome'

     _c_n_C_o_n_f_i_d_e_n_c_e 'signature(object = "SnpLevelSet")': Accessor for
          matrix of confidence scores for the copy number estimates.

     _c_n_C_o_n_f_i_d_e_n_c_e<- 'signature(object = "SnpLevelSet", value =
          "matrix")': Replacement method for confidence scores of copy
          number estimates.

     _c_o_m_b_i_n_e 'signature(x = "SnpLevelSet", y = "SnpLevelSet")': Useful
          for combining two objects with the same 'phenoData'. For
          instance, combine an object created from the Hind 50k chip
          and an object created from the Xba 50k chip.

     _c_o_p_y_N_u_m_b_e_r 'signature(object = "SnpLevelSet")': Accessor for
          matrix of copy numbers.

     _c_o_p_y_N_u_m_b_e_r<- 'signature(object = "SnpLevelSet", value =
          "matrix")': Replacement method for copy number matrices

     _d_b 'signature(object = "SnpLevelSet")': See also 'db'

     _p_o_s_i_t_i_o_n 'signature(object = "SnpLevelSet")': See also 'position'

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

     RS

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

     showClass("SnpLevelSet")

