genotypeEmission         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 _d_i-_a_l_l_e_l_i_c _g_e_n_o_t_y_p_e _c_a_l_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Emission probabilities for di-allelic genotype calls

_U_s_a_g_e:

     genotypeEmission(genotypes, conf, states, probHomCall, probMissing, verbose=TRUE)

_A_r_g_u_m_e_n_t_s:

genotypes: matrix of integers (1=AA, 2=AB, 3=BB, 4=other)

    conf: Confidence estimates of the genotype calls obtained from
          crlmm (optional).

  states: character string of hidden states

probHomCall: numeric: probability of a homozygous genotype call
          specified in the same order as the hidden states

probMissing: numeric: probability of a missing genotype call specified
          in the same order as the hidden states

 verbose: logical

_D_e_t_a_i_l_s:

     CRLMM provides confidences estimates of the genotype calls that
     can be integrated to improve the HMM.  Because CRLMM will genotype
     all SNPs, the probMissing argument is unecessary.

_V_a_l_u_e:

   array: Array of emission probabilities.  Dimension 1: SNPs,
          Dimension 2: samples, Dimension3: states

