findBreaks            package:VanillaICE            R Documentation

_I_d_e_n_t_i_f_y _b_r_e_a_k_p_o_i_n_t_s _f_r_o_m _t_h_e _h_i_d_d_e_n _M_a_r_k_o_v _m_o_d_e_l _p_r_e_d_i_c_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Identify breakpoints: physical position of breaks, number of SNPs
     in region, and the called hidden state.

_U_s_a_g_e:

     findBreaks(x, states, position, chromosome, sample, lik1, lik2)

_A_r_g_u_m_e_n_t_s:

       x: matrix of predicted hidden states (integer)

  states: character string giving the hidden states

position: physical position of the SNPs

chromosome: chromosome number

  sample: sample name

    lik1: likelihood under alternative model

    lik2: likelihood under NULL model

_V_a_l_u_e:

data.frame: data.frame describing regions of normal and altered states

