crlmm                 package:oligo                 R Documentation

_G_e_n_o_t_y_p_e _C_a_l_l_s

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

     Performs genotype calls via CRLMM (Corrected Robust Linear Model
     with Maximum-likelihood based distances).

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

     crlmm(object, correction = NULL, recalibrate = TRUE, minLLRforCalls = c(25, 5, 25), verbose = TRUE, correctionFile = NULL)

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

  object: 'SnpQSet' object

correction: The output of the EM algorithm

recalibrate: Logical - should recalibration be performed?

minLLRforCalls: Minimum thresholds for genotype calls.

 verbose: Logical.

correctionFile: A filename.

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

     The 'correctionFile' is a string (eg, "outputEM.rda") pointing to
     a filename. If the file does not exist, 'crlmm' will save a file
     with that name containing the results of the EM algorithm. If the
     file exists, its content is loaded and used by CRLMM. The
     'correctionFile' is meant to save time if 'crlmm' is be run
     multiple times, as the EM algorithm does not need to be run
     everytime.

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

     'SnpCallSet' object.

_N_o_t_e:

_A_u_t_h_o_r(_s):

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

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

