findTrans.func             package:aCGH             R Documentation

_F_u_n_t_i_o_n _i_d_e_n_t_i_f_y_i_n_g _t_h_e _t_r_a_n_s_i_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function identifies the start and end of the states (regions
     with the constant estimated copy number).

_U_s_a_g_e:

     findTrans.func(outliers = res1$outliers, aber = res2$aber, statesres =
     states.bic)

_A_r_g_u_m_e_n_t_s:

outliers: Binary matrix of the outliers (generally output of the
          'findOutliers.func')

    aber: Binary matrix of the focal aberrations (generally output of
          the 'findAber.func')

statesres: The states output of the 'hmm.run.func'

_D_e_t_a_i_l_s:

     The transitions end is placed at the last non-focal aberration
     clone of the contiguous region containing clones belonging to the
     same state and transitions start is placed at the first non-focal
     aberration clone of the contiguous region containing clones
     belonging to the same state.

_V_a_l_u_e:

trans.matrix: Matrix with a row for each clone and column for each
          sample. The starts of the states are indicated by "1" , the
          end are by "2" and the focal aberrations are coded as "3"

translen.matrix: Matrix with a row for each clone and column for each
          sample. The entries are the length of the region to which a
          clone belongs. Zero length is assigned to the focal
          aberrations. This output may be buggy at the moment.

_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'

