hapmapProbabilities        package:VanillaICE        R Documentation

_C_R_L_M_M _c_o_n_f_i_d_e_n_c_e _s_c_o_r_e_s _o_n _H_a_p_M_a_p _d_a_t_a

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

     Wrapper for extracting the chip-specific distribution of CRLMM
     confidence scores for HapMap data where we assume we know the true
     genotype. Presently only supported for Affymetrix 50k and 250k SNP
     chips and onnly relevant for fitting the ICE HMM (see reference
     below).

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

     hapmapProbabilities(x)

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

       x: Name of chip. Must be 'pd.mapping...'

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

     Confidence scores in a 'SnpCallSet' created by 'crlmm' are stored
     in the element "pAcc" in the assay data.

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

     Matrix of confidence scores

_N_o_t_e:

_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:

     'crlmm', 'SnpCallSet-class', 'AssayDataElement'

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

