mergeFunc                package:aCGH                R Documentation

_F_u_n_t_i_o_n _t_o _m_e_r_g_e _s_t_a_t_e_s _b_a_s_e_d _o_n _t_h_e_i_r _s_t_a_t_e _m_e_a_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     'mergeFunc' takes the output of hmm.run.func (or find.hmm.states)
     with a particular model selection criterion and iteratively merges
     the states with means closer than a supplied threshold.
     'mergeHmmStates' is a frontend for 'mergeFunc' using 'aCGH'
     object.

_U_s_a_g_e:

     mergeHmmStates(aCGH.obj, model.use = 1, minDiff = 0.25)
     mergeFunc(statesres = states.bic, minDiff = 0.1)

_A_r_g_u_m_e_n_t_s:

aCGH.obj: Object of class 'aCGH'. 

statesres: the sublist of the states.hmm list output from
          'find.hmm.states' for a given model selection crterion 

 minDiff: The states whose predicted values are less than minDiff apart
          are merged into one state and all the predicited values are
          recomputed. 

model.use: Model selection criterion to use, See 'find.hmm.states'. 

_D_e_t_a_i_l_s:

     This function is intended to reduce effect of the possible small
     magnitude technological artifacts on the structure determination.

_V_a_l_u_e:

     List containing states.hmm object is returned.

_A_u_t_h_o_r(_s):

     Jane Fridlyand

_R_e_f_e_r_e_n_c_e_s:

     Application of Hidden Markov Models to the analysis of the array
     CGH data, Fridlyand et.al., _JMVA_, 2004

_S_e_e _A_l_s_o:

     'aCGH', 'find.hmm.states'

