calls                 package:crlmm                 R Documentation

_A_c_c_e_s_s_o_r_s _f_o_r _C_a_l_l_s _a_n_d _C_o_n_f_i_d_e_n_c_e_s _o_n _a _S_n_p_S_e_t _o_b_j_e_c_t

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

     'calls' returns the genotype calls. CRLMM stores genotype calls as
     integers (1 - AA; 2 - AB; 3 - BB).

     'confs' returns the confidences associated to the genotype calls.
     THe current implementation of CRLMM stores the confidences as
     integers by using the transformation:

     conf = round(-1000*log2(1-p)),

     where 'p' is the posterior probability of the call.

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

     calls(x)
     confs(x)

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

       x: SnpSet object

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

     Matrix of genotype calls or confidences.

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

       set.seed(1)
       theCalls <- matrix(sample(1:3, 20, rep=TRUE), nc=2)
       p <- matrix(runif(20), nc=2)
       theConfs <- round(-1000*log2(1-p))
       obj <- new("SnpSet", call=theCalls, callProbability=theConfs)
       calls(obj)
       confs(obj)

