HmmOptions-class         package:VanillaICE         R Documentation

_C_l_a_s_s "_H_m_m_O_p_t_i_o_n_s"

_D_e_s_c_r_i_p_t_i_o_n:

     Options for fitting the hidden Markov model.

_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("HmmOptions",
     snpset, states, copyNumber.location, copyNumber.scale,
     copyNumber.ICE, calls.ICE, probHomCall, term5)'.

_S_l_o_t_s:


     '_s_t_a_t_e_s': Object of class '"character"'.  Hidden states of the
          HMM.

     '_s_n_p_s_e_t': '"SnpLevelSet"' instance. 

     '_c_o_p_y_N_u_m_b_e_r._l_o_c_a_t_i_o_n': Object of class '"numeric"'.  Ignored when
          snpset is an instance of 'SnpCallSet'. See
          'copyNumber.location'

     '_c_o_p_y_N_u_m_b_e_r._s_c_a_l_e': Object of class '"NULLOrNumeric"'.  This slot
          is not currently used.  If one has standard errors for the
          copy number estimates, the inverse of the standard errors
          should be stored in the 'cnConfidence' 'assayData' element of
          the snpset object.

     '_c_o_p_y_N_u_m_b_e_r._I_C_E': Object of class '"logical"'. See
          'copyNumber.ICE'.  

     '_c_a_l_l_s._I_C_E': Object of class '"logical"'.  See 'calls.ICE'

     '_p_r_o_b_H_o_m_C_a_l_l': Object of class '"numeric"'. The probability of a
          homozygous genotype call corresponding to each of the states.
          When 'calls.ICE' is TRUE, only the first two elements will be
          used.

     '_t_e_r_m_5': Object of class '"NULLOrNumeric"'. User-specified
          probabilities of f(HOM | genotype call, state).  Ignored when
          'calls.ICE' is 'FALSE'.  For more details, see Equation 2.7
          in the manuscript that this package references.

_M_e_t_h_o_d_s:



     [ 'signature(x = "HmmOptions")': 

     _a_n_n_o_t_a_t_i_o_n 'signature(object = "HmmOptions")': 

     _a_n_n_o_t_a_t_i_o_n<- 'signature(object = "HmmOptions", value = "ANY")': 

     _c_a_l_c_u_l_a_t_e_D_i_s_t_a_n_c_e 'signature(object = "HmmOptions")': 

     _c_a_l_l_s._I_C_E 'signature(object = "HmmOptions")': 

     _c_a_l_l_s._I_C_E<- 'signature(object = "HmmOptions", value="logical")':               

     _c_o_p_y_N_u_m_b_e_r._I_C_E 'signature(object = "HmmOptions")': 

     _c_o_p_y_N_u_m_b_e_r._I_C_E<- 'signature(object = "HmmOptions",
          value="logical")':         

     _d_b 'signature(object = "HmmOptions")': 

     _h_m_m 'signature(object = "HmmOptions", params = "HmmParameter")':

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "HmmOptions")': 

     _n_o_t_e_s 'signature(object = "HmmOptions")': 

     _s_h_o_w 'signature(object = "HmmOptions")':  

     _s_t_a_t_e_s 'signature(object = "HmmOptions")':  

     _s_t_a_t_e_s<- 'signature(object = "HmmOptions", value = "character")': 

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     'HmmParameter-class'

_E_x_a_m_p_l_e_s:

     showClass("HmmOptions")

