genotypeEmissionCrlmm       package:VanillaICE       R Documentation

_E_s_t_i_m_a_t_e _t_h_e _e_m_i_s_s_i_o_n _p_r_o_b_a_b_i_l_i_t_i_e_s _u_s_i_n_g _c_o_n_f_i_d_e_n_c_e _s_c_o_r_e_s _f_r_o_m _C_R_L_M_M

_D_e_s_c_r_i_p_t_i_o_n:

     Estimate the emission probabilities that incorporate information
     on the confidence scores for the genotype calls.

_U_s_a_g_e:

     genotypeEmissionCrlmm(genotypes, conf, pHetCalledHom = 0.001, pHetCalledHet = 0.995, pHomInNormal = 0.99, pHomInRoh = 0.999, annotation)

_A_r_g_u_m_e_n_t_s:

genotypes: Matrix of genotypes

    conf: Matirx of confidence scores (see details).

pHetCalledHom: The probability that a truly heterozygous SNP is
          incorrectly called homozygous (incorrect call).

pHetCalledHet: The probability that a truly heterozygous SNP is called
          heterozygous (correct call).

pHomInNormal: The probability of a homozygous genotype call in the
          'normal' state.

pHomInRoh: The probability of a homozygous genotype call in a region of
          homozygosity.

annotation: The cdf name (e.g., "genomewidesnp6")

_D_e_t_a_i_l_s:

     The confidence scores by crlmm are saved as an integer:
     1000*log(1-p), where p is the probability that the genotype call
     is correct.

     The reference distribution of confidence scores are available for
     the following Affymetrix platforms: affy6, nsp250, and sty250k.

_V_a_l_u_e:

     An R x C x X array of emission probabilities, where

     R = number of loci (SNPs) C = number of samples S = number of
     states

_A_u_t_h_o_r(_s):

     R Scharpf

_R_e_f_e_r_e_n_c_e_s:

     RB Scharpf et al. (2008), Annals of Applied Statistics

