plot_theta               package:RLMM               R Documentation

_A_l_l_e_l_e _S_u_m_m_a_r_y _P_l_o_t

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

     Creates an Allele Summary plot (allele B vs. allele A) for each
     SNP specified in snpsfilename. The points in the plot are the
     (theta A, theta B) ordered pairs for all the samples of the SNP.
     If a plotfilename is specified,  it will save the plot as a .ps
     file, otherwise the plot is shown on screen.

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

     plot_theta(genotypefile = "Xba.rlmm",
                thetafile = "Xba.theta",
                Pick.Obj = "FALSE",
                plotfile = "plots.ps",
                snpsfile = "snps.lst")

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

genotypefile: Character string specifying the directory AND name of the
          .rlmm file created by 'Classify' (optional)

thetafile: Character string specifying the directory AND name of the
          .rlmm file created by 'Create_Thetafile' (optional)

Pick.Obj: At this point, it should always be left as the default FALSE,
          ie: it is for development purposes only (optional)

plotfile: The name where to store the plot as a .ps file, if blank such
          as "", it will display on screen instead (optional)

snpsfile: A list of SNPs to plot, with one SNP following another on a
          newline (optional)

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

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

