badorder                 package:qtl                 R Documentation

_A_n _i_n_t_e_r_c_r_o_s_s _w_i_t_h _m_i_s_p_l_a_c_e_d _m_a_r_k_e_r_s

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

     Simulated data for an intercross with some markers out of order.

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

     data(badorder)

_F_o_r_m_a_t:

     An object of class 'cross'.  See 'read.cross' for details.

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

     There are 250 F2 individuals typed at a total of 36 markers on
     four chromosomes.  The data were simulated with QTLs at the center
     of chromosomes 1 and 3. 

     The order of several markers on chromosome 1 is incorrect. 
     Markers on chromosomes 2 and 3 are switched.

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

     Karl W Broman, kbroman@jhsph.edu

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

     'est.rf', 'ripple',  'est.map', 'sim.cross'

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

     data(badorder)


     # estimate recombination fractions
     badorder <- est.rf(badorder)
     plot.rf(badorder)

     # re-estimate map
     newmap <- est.map(badorder)
     plot.map(badorder,newmap)

     # assess marker order on chr 1
     rip3 <- ripple(badorder,1,window=3)
     summary(rip3)

