copyNumber.ICE          package:VanillaICE          R Documentation

_I_n_d_i_c_a_t_e_s _w_h_e_t_h_e_r _t_o _u_s_e _c_o_n_f_i_d_e_n_c_e _s_c_o_r_e_s _o_f _t_h_e _o_b_s_e_r_v_e_d _c_o_p_y
_n_u_m_b_e_r _e_s_t_i_m_a_t_e_s _i_n _t_h_e _H_M_M

_D_e_s_c_r_i_p_t_i_o_n:

     In the current framework, the confidence scores are assumed to be
     the inverse of the standard error

_U_s_a_g_e:

     copyNumber.ICE(object)
     copyNumber.ICE(object) <- value

_A_r_g_u_m_e_n_t_s:

  object: An object of class 'HmmOptions'

   value: Logical. If TRUE, confidence scores of the copy number
          estimates are used to calculate emission probabilities.

_D_e_t_a_i_l_s:

     If TRUE, the confidence scores (assumed to be inverse standard
     errors) are used by the hidden Markov model.  This has the
     desirable consequence of providing more local smmoothing for
     precise estimates of copy number and more global smoothing for
     copy number estimates with higher standard errors. When FALSE, a
     robust estimate of the chip variability is calculated across all
     of the autosomes.

_V_a_l_u_e:

     Logical

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     See the VanillaICE vignette

