getHapmapProbabilities      package:VanillaICE      R Documentation

_E_s_t_i_m_a_t_e _p_r_o_b_a_b_i_l_i_t_y _o_f _c_o_r_r_e_c_t _g_e_n_o_t_y_p_e _c_a_l_l

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

     This function is used by the ICE HMM described in the reference
     below and currently only supported for 50k and 250k Affymetrix SNP
     chips.  A nonparametric estimate of the probability that the
     genotype call is correct is based on the distribution of 'crlmm'
     confidence scores in the reference HapMap population, where we
     assume that we know the true genotype.  A similar approach could
     be used to estimate probabilities with other genotyping
     algorithms.  See reference below for more information.

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

     getHapmapProbabilities(object)

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

  object: One of the HMM classes defined in 'ICE'

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

     The annotation slot in the object must contain one of the
     following strings that identifies the Affymetrix chip:

     mapping100k (if the 50k xba and 50k hind results have been merged
     into one object)

     pd.mapping50k.xba240  (50k Xba platform)

     pd.mapping50k.hind240 (50k Hind)

     mapping500k  (if the two 250k chips - Nsp and Sty - have been
     merged)

     pd.mapping250k.nsp

     pd.mapping250k.sty

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

     A vector of probabilities that the genotype call is correct.

_N_o_t_e:

     Estimated probabilities are chip-specific.  This function is
     typically not 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:

     'callEmission', 'crlmm'

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

