HmmSnpSet-class          package:VanillaICE          R Documentation

_H_m_m_S_n_p_S_e_t

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

_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("HmmSnpSet",
     assayData, featureData, phenoData, experimentData, annotation,
     calls, callsConfidence, copyNumber, cnConfidence, predictions,
     scaleCopyNumber, probabilityCalledHomIfNormal,
     probabilityCalledHetIfLoh, log2, locationCopyNumber, stateNames,
     ...)'.

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

     '_l_o_c_a_t_i_o_n_C_o_p_y_N_u_m_b_e_r': Object of class '"numeric"'  

     '_s_c_a_l_e_C_o_p_y_N_u_m_b_e_r': Object of class '"NullOrMatrix"'  

     '_l_o_g_2': Object of class '"logical"'  

     '_p_r_e_d_i_c_t_i_o_n_s': Object of class '"matrix"'  

     '_d_i_s_t_a_n_c_e': Object of class '"logical"'  

     '_i_n_i_t_i_a_l_S_t_a_t_e_P_r_o_b_a_b_i_l_i_t_y': Object of class '"NullOrNumeric"'  

     '_t_r_a_n_s_i_t_i_o_n_P_r_o_b_a_b_i_l_i_t_y': Object of class '"NullOrNumericOrMatrix"'            

     '_e_m_i_s_s_i_o_n_P_r_o_b_a_b_i_l_i_t_y': Object of class '"NullOrMatrix"'  

     '_l_i_k_e_l_i_h_o_o_d': Object of class '"NullOrMatrix"'  

     '_c_h_r_o_m_o_s_o_m_e_A_r_m': Object of class '"character"'  

     '_c_a_l_l_s_I_c_e': Object of class '"logical"'      

     '_c_o_p_y_N_u_m_b_e_r_I_c_e': Object of class '"logical"'      

     '_s_t_a_t_e_N_a_m_e_s': Object of class '"character"'  

     '_c_h_r_o_m_o_s_o_m_e_A_n_n_o_t_a_t_i_o_n': Object of class '"data.frame"'  

     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"'  

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

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class '"AnnotatedDataFrame"'  

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class '"MIAME"'  

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"'  

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

     '_p_r_o_b_a_b_i_l_i_t_y_C_a_l_l_e_d_H_o_m_I_f_N_o_r_m_a_l': Object of class '"numeric"'  

     '_p_r_o_b_a_b_i_l_i_t_y_C_a_l_l_e_d_H_e_t_I_f_L_o_h': Object of class '"numeric"'  

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

     Class 'HmmSnpCopyNumberSet-class', directly. Class
     'HmmSnpCallSet-class', directly. Class 'hSet-class', by class
     "HmmSnpCopyNumberSet", distance 2. Class 'AnnotatedSnpSet-class',
     by class "HmmSnpCopyNumberSet", distance 3. Class
     'AnnotatedSnpCallSet-class', by class "HmmSnpCopyNumberSet",
     distance 4. Class 'AnnotatedSnpCopyNumberSet-class', by class
     "HmmSnpCopyNumberSet", distance 4, with explicit coerce. Class
     'SnpCallSet-class', by class "HmmSnpCopyNumberSet", distance 5.
     Class 'class.eSet', by class "HmmSnpCopyNumberSet", distance 6.
     Class 'VersionedBiobase-class', by class "HmmSnpCopyNumberSet",
     distance 7. Class 'Versioned-class', by class
     "HmmSnpCopyNumberSet", distance 8. Class 'SnpCopyNumberSet-class',
     by class "HmmSnpCopyNumberSet", distance 5, with explicit coerce.
     Class 'class.eSet', by class "HmmSnpCopyNumberSet", distance 6,
     with explicit coerce. Class 'VersionedBiobase-class', by class
     "HmmSnpCopyNumberSet", distance 7, with explicit coerce. Class
     'Versioned-class', by class "HmmSnpCopyNumberSet", distance 8,
     with explicit coerce. Class 'hSet-class', by class
     "HmmSnpCallSet", distance 2. Class 'AnnotatedSnpSet-class', by
     class "HmmSnpCallSet", distance 3. Class
     'AnnotatedSnpCallSet-class', by class "HmmSnpCallSet", distance 4.
     Class 'AnnotatedSnpCopyNumberSet-class', by class "HmmSnpCallSet",
     distance 4, with explicit coerce. Class 'SnpCallSet-class', by
     class "HmmSnpCallSet", distance 5. Class 'class.eSet', by class
     "HmmSnpCallSet", distance 6. Class 'VersionedBiobase-class', by
     class "HmmSnpCallSet", distance 7. Class 'Versioned-class', by
     class "HmmSnpCallSet", distance 8. Class 'SnpCopyNumberSet-class',
     by class "HmmSnpCallSet", distance 5, with explicit coerce. Class
     'class.eSet', by class "HmmSnpCallSet", distance 6, with explicit
     coerce. Class 'VersionedBiobase-class', by class "HmmSnpCallSet",
     distance 7, with explicit coerce. Class 'Versioned-class', by
     class "HmmSnpCallSet", distance 8, with explicit coerce.

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

     [ 'signature(x = "HmmSnpSet")': ... 

     [<- 'signature(x = "HmmSnpSet")': ... 

     _b_r_e_a_k_p_o_i_n_t_s 'signature(object = "HmmSnpSet")': ... 

     _c_a_l_c_u_l_a_t_e_E_m_i_s_s_i_o_n_P_r_o_b_a_b_i_l_i_t_y 'signature(object = "HmmSnpSet")':
          ... 

     _c_o_e_r_c_e 'signature(from = "AnnotatedSnpSet", to = "HmmSnpSet")':
          ... 

     _c_a_l_l_s_I_c_e 'signature(object = "HmmSnpSet")': ... 

     _c_o_p_y_N_u_m_b_e_r_I_c_e 'signature(object = "HmmSnpSet")': ...     

     _g_e_t_C_o_p_y_N_u_m_b_e_r_L_o_c_a_t_i_o_n 'signature(object = "HmmSnpSet")': ... 

     _g_e_t_L_o_h_P_r_o_b_a_b_i_l_i_t_y 'signature(object = "HmmSnpSet")': ... 

     _g_e_t_T_r_a_n_s_i_t_i_o_n_P_r_o_b_a_b_i_l_i_t_y 'signature(object = "HmmSnpSet")': ... 

     _h_m_m 'signature(object = "HmmSnpSet")': ... 

     _i_c_e_2_V_a_n_i_l_l_a_I_C_E 'signature(.Object = "HmmSnpSet")': Resets the
          package attribute from ICE (DEPRECATED package name) to
          VanillaICE

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

     _l_o_c_a_t_i_o_n_C_o_p_y_N_u_m_b_e_r 'signature(object = "HmmSnpSet")': ... 

     _l_o_c_a_t_i_o_n_C_o_p_y_N_u_m_b_e_r<- 'signature(object = "HmmSnpSet")': ... 

     _p_l_o_t_H_m_m 'signature(object = "HmmSnpSet")': ... 

     _p_r_e_d_i_c_t_i_o_n_s 'signature(object = "HmmSnpSet")': ... 

     _p_r_e_d_i_c_t_i_o_n_s<- 'signature(object = "HmmSnpSet", value = "matrix")':
          ... 

     _s_c_a_l_e_C_o_p_y_N_u_m_b_e_r 'signature(object = "HmmSnpSet")': ... 

     _s_c_a_l_e_C_o_p_y_N_u_m_b_e_r<- 'signature(object = "HmmSnpSet")': ... 

     _s_h_o_w 'signature(object = "HmmSnpSet")': ... 

_N_o_t_e:

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

     Robert Scharpf

_R_e_f_e_r_e_n_c_e_s:

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

     'HmmSnpCopyNumberSet-class', 'HmmSnpCallSet-class' 'hSet-class'

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

     showClass("HmmSnpSet")

