getCopyNumberScale        package:VanillaICE        R Documentation

_S_c_a_l_e _p_a_r_a_m_e_t_e_r _u_s_e_d _f_o_r _G_a_u_s_s_i_a_n _d_i_s_t_r_i_b_u_t_i_o_n _o_f _c_o_p_y _n_u_m_b_e_r

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

     We typically assume that after appropriate transformation the
     distribution of copy number is approximately Gaussian.  This
     function calculates a robust estimate of the spread based on
     quantiles of the observed copy number distribution across all
     autosomes.

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

     getCopyNumberScale(object, ...)

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

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

     ...: additional arguments for subsetting the samples

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

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

     A vector of scales with length equal to the number of hidden
     states (typically 3 or 4)

_N_o_t_e:

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

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

     RB Scharpf et al. (2007), Department of Biostatistics Working
     Papers, Working Paper 136

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

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

