findAberrations           package:snapCGH           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:

     findAberrations(segList, maxClones = 1, maxLen = 1000)

_A_r_g_u_m_e_n_t_s:

 segList: An object of class SegList

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

_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

