create_Thetafile            package:RLMM            R Documentation

_C_a_l_c_u_l_a_t_i_n_g _P_a_r_a_m_e_t_e_r _E_s_t_i_m_a_t_e_s

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

     Assuming that the *.norm files are created, this step of the data
     analysis will calculate estimates of theta A and theta B values
     for each SNP and chip based on normalized probe intensity data
     from the *.norm files. The theta values are produced from fitting
     a probe-level additive model to the log2 A probe intensities and
     the B intensities separately.

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

     create_Thetafile(probefiledir = getwd(),
                      start = 1,
                      end = -1,
                      thetafile = "")

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

probefiledir: Character string specifying the directory with the *.norm
          files (optional)

   start: An integer value specifying which SNP number we should start
          at when calculating the theta values (optional)

     end: An integer value specifying which SNP number we should stop
          at when calculating the theta values (optional)

thetafile: A character string specifying the name the theta file will
          be saved as (optional)

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

     Nusrat Rabbee <nrabbee@post.harvard.edu>, Gary Wong
     <wongg62@gmail.com>

