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'

