findAber.func              package:aCGH              R Documentation

_F_u_n_c_t_i_o_n _t_o  _d_e_t_e_r_m_i_n_e_s _f_o_c_a_l _a_b_e_r_r_a_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function identifies clones that are focal aberrations.

_U_s_a_g_e:

     findAber.func(maxClones = 1, maxLen = 1000, statesres = states.bic)

_A_r_g_u_m_e_n_t_s:

maxClones: Maximum number of clones assigned to the same state which
          can be considered to be focal aberrations

  maxLen: Maximum lengeth of the region containing clones assigned to
          the state so that those clones can be considered to be focal
          aberrations

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

_D_e_t_a_i_l_s:

     The focal aberrations are the one or more clones assigned to the
     state different from the states of the surrounding clones.  They
     may indicate copy number polymorphisms or interesting high or low
     focal changes.

_V_a_l_u_e:

    aber: Binary matrix with a row for each clone and column for each
          sample. 1 indicates presence of a focal aberrations, 0 lack
          of such.

_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

