getCopyNumberLocation       package:VanillaICE       R Documentation

_T_y_p_i_c_a_l_l_y _t_h_e _m_e_a_n _c_o_p_y _n_u_m_b_e_r _f_o_r _t_h_e _h_i_d_d_e_n _s_t_a_t_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Use to provide default values of the copy number for the hidden
     states.  We typically assume that the distribution of the observed
     copy number (after suitable transformation) is approximately
     Gaussian and centered at the true copy number.

_U_s_a_g_e:

     getCopyNumberLocation(object)

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

  object: An object of class 'HmmSnpSet' or 'HmmSnpCopyNumberSet'

_D_e_t_a_i_l_s:

     By default, we assume that the true underlying copy number for a
     deletion is 1, 2 for a normal region (diploid), and 3 for an
     amplification.

_V_a_l_u_e:

     numerical vector of locations for the Gaussian distribution for
     copy number

_N_o_t_e:

     Not typically called directly

_A_u_t_h_o_r(_s):

     who you are

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s:

