mergeStates             package:snapCGH             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:

     'mergeStates' takes the output of a segementation algorithm in the
     form of a 'SegList' and iteratively merges the states with means
     closer than a supplied threshold.

_U_s_a_g_e:

     mergeStates(segList, MergeType = 1, pv.thres=0.0001, ansari.sign=0.01, minDiff = 0.25)

_A_r_g_u_m_e_n_t_s:

 segList: Object of class 'SegList'. 

MergeType: Select either 1 or 2.  1 uses a new merging algorithm
          developed by Hanni Willenbrock and Jane Fridlyand. 

pv.thres: Significance threshold for Wilcoxon test for level merging. 
          Used when MergeType = 1.

ansari.sign: Significance threshold for Ansari-Bradley test. Used when
          MergeType = 1.

 minDiff: The states whose predicted values are less than minDiff apart
          are merged into one state and all the predicited values are
          recomputed.  Used when MergeType = 2.    

_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:

     A 'SegList' object is returned with the merged states stored in
     the 'pred' list.

_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:

     'SegList', 'runHomHMM', 'runGLAD', 'runDNAcopy'

