getCallEmission          package:VanillaICE          R Documentation

_C_a_l_c_u_l_a_t_e_s _e_m_i_s_s_i_o_n _p_r_o_b_a_b_i_l_i_t_i_e_s _f_o_r _g_e_n_o_t_y_p_e _c_a_l_l_s

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

     Calculates emission probabilities for genotype calls. Only used by
     the ICE HMM.

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

     getCallEmission(object, CALL.STATES = 2, SAMPLE = 1, P.HOM.CHOM = 0.999,
     P.HET.CHOM = 1 - 0.999, P.HET.CHET = 0.999, P.HOM.CHET = 1 - 0.999,
     P.CHOM.Normal, P.CHOM.LOH, hapmapP)

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

  object: Typically an object of class 'HmmSnpCallSet' 

CALL.STATES: Integer: number of hidden states (default is 2 - loss of
          heterozygosity and retention of heterozygosity)

  SAMPLE: Integer: which sample to extract genotype calls from the
          'HmmSnpCallSet' object

P.HOM.CHOM: Numeric. Probability that the true genotype is homozygous
          (AA or BB) given that the observed genotype was homozygous
          (AA or BB)

P.HET.CHOM: Numeric. Probability that the true genotype is heterozygous
          (AB) given that the observed genotype was homozygous.

P.HET.CHET: Numeric. Probability that the true genotype is heterozygous
          (AB) given that the observed genotype was heterozygous. 

P.HOM.CHET: Numeric. Probability that the true genotype is homozygous
          given that the observed genotype was heterozygous. 

P.CHOM.Normal: Numeric. Probability that the observed genotype is
          homozygous if the true hidden state is retention of
          heterozygosity.

P.CHOM.LOH: Numeric. Probability that the observed genotype is
          homozygous given that the true hidden state is loss of
          heterozygosity.

 hapmapP: A matrix estimated from 269 HapMap samples.  See details.

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

     We group the CRLMM probabilities of a correct genotype call for
     the 269 HapMap samples into 1 of 4 possible categories:

     1:  genotype call is HET, truth is HOM 2:  genotype call is HET,
     truth is HET 3:  genotype call is HOM, truth is HOM 4:  genotype
     call is HOM, truth is HET

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

     Returns matrix of emission probabilities that are a function of
     the confidence scores provided by 'crlmm' for genotype calls.

_N_o_t_e:

     Not typically called directly.

_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:

     The R package 'callsConfidence': <URL:
     http://www.biostat.jhsph.edu/~rscharpf/software/index.html>

     'callEmission', 'hmm', 'crlmm'

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

