snpm2mapLD              package:GGtools              R Documentation

_p_r_e_p_a_r_e _i_n_p_u_t _t_o _m_a_p_L_D _f_u_n_c_t_i_o_n _f_o_r _h_a_p_l_o_t_y_p_e _b_l_o_c_k _i_d_e_n_t_i_f_i_c_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     prepare input to mapLD function for haplotype block identification

_U_s_a_g_e:

     snpm2mapLD(x, chrnum, runMAP=TRUE, ...)

_A_r_g_u_m_e_n_t_s:

       x: snp.matrix instance

  chrnum: chromosome number

  runMAP: logical indicating whether or not to run mapLD

     ...: additional arguments to mapLD

_D_e_t_a_i_l_s:

     sets up a data frame suitable for mapLD, and will invoke with
     appropriate arguments identifying columns for alleles and other
     identifiers if runMAP is TRUE (default).

     smtest is a small snp.matrix instance

_V_a_l_u_e:

     a list with element struc holding the data frame, and mapLD output
     if requested.  Note that mapLD writes an eps file to disk *sigh*.

_A_u_t_h_o_r(_s):

     Vince Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     data(smtest)
     ss = snpm2mapLD(smtest, chrnum=20, runMAP=FALSE)
     ss
     # you could run mapLD on ss[[1]]

