copynumberEmission        package:VanillaICE        R Documentation

_E_m_i_s_s_i_o_n _p_r_o_b_a_b_i_l_i_t_i_e_s _f_o_r _c_o_p_y _n_u_m_b_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     Emission probabilities for copy number

_U_s_a_g_e:

     copynumberEmission(copynumber, states, mu, sds, takeLog, verbose = TRUE,
     na.rm=TRUE)

_A_r_g_u_m_e_n_t_s:

copynumber: matrix

  states: character string

      mu: numeric: mean of hidden states for Gaussian

     sds: standard deviations of copy number estimates

 takeLog: logical: if TRUE, this function takes the log of the copy
          number AND mu arguments to this function

 verbose: logical

   na.rm: The default is to ignore missing values when calculating
          robust standard deviations

_D_e_t_a_i_l_s:

     By default, this func estimates the scale parameter for the Normal
     distribution from the supplied data using the median absolute
     deviation (MAD). However, different standard deviations can be
     supplied by the user with the argument 'sds'. The supplied
     standard deviations must be of the same dimension as the copy
     number matrix.

_V_a_l_u_e:

   array: Array of emission probabilities on the log scale. Dimension
          1: SNPs, Dimension 2: samples, Dimension3: states

_S_e_e _A_l_s_o:

     'genotypeEmission', 'genotypeEmissionCrlmm'

