HmmPredict-class         package:VanillaICE         R Documentation

_C_l_a_s_s _f_o_r _t_h_e _h_i_d_d_e_n _M_a_r_k_o_v _m_o_d_e_l _r_e_s_u_l_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Contains the predictions for the hidden states and a list of
     breakpoint matrices.  Each element in the list corresponds to the
     breakpoints identified in one sample.

_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("HmmPredict",
     states, predictions, breakpoints, SnpClass)'.

_S_l_o_t_s:


     '_s_t_a_t_e_s': Object of class 'character'. Character string of the
          hidden states.

     '_p_r_e_d_i_c_t_i_o_n_s': Object of class 'matrix'. Matrix of predictions.

     '_b_r_e_a_k_p_o_i_n_t_s': Object of class 'list'.  List of matrices.  Each
          element is the matrix of breakpoints for one sample.

     '_S_n_p_C_l_a_s_s': Object of class 'character'. The class of SNP data
          (e.g., 'oligoSnpSet') 

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class 'AnnotatedDataFrame'

_M_e_t_h_o_d_s:


     _S_n_p_C_l_a_s_s 'signature(object = "HmmPredict")': Accessor for class of
          SNP data

     [ 'signature(x = "HmmPredict")': Subsetting the predictions

     _b_r_e_a_k_p_o_i_n_t_s 'signature(object = "HmmPredict")': Accessor for the
          list of breakpoints

     _b_r_e_a_k_p_o_i_n_t_s<- 'signature(object = "HmmPredict", value =
          "data.frame")': Replacement method for breakpoints    

     _f_D_a_t_a 'signature(object="HmmPredict")': Accessor for the data
          frame of all feature-level (SNP-level) annotation (e.g.,
          physical position)

     _f_e_a_t_u_r_e_D_a_t_a 'signature(object = "HmmPredict")': Accessor for the
          featureData

     _f_e_a_t_u_r_e_N_a_m_e_s 'signature(object = "HmmPredict")': Character string
          of SNP identifiers

     _g_e_t_P_a_r 'signature(object = "HmmPredict")': Graphical parameters.

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "HmmPredict")'  

     _p_o_s_i_t_i_o_n 'signature(object = "HmmPredict")': Accessor for the
          physical position of SNPs in the object 'HmmPredict'

     _p_r_e_d_i_c_t_i_o_n_s 'signature(object = "HmmPredict")': Accessor for the
          predictions

     _p_r_e_d_i_c_t_i_o_n_s<- 'signature(object = "HmmPredict", value="matrix")':
          Replacement method for predictions    

     _s_a_m_p_l_e_N_a_m_e_s 'signature(object = "HmmPredict")': Sample names

     _s_h_o_w 'signature(object = "HmmPredict")'

     _s_t_a_t_e_s 'signature(object = "HmmPredict")': Accessor for hidden
          states

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     'hmm'

_E_x_a_m_p_l_e_s:

     showClass("HmmPredict")

