checkAlleles               package:qtl               R Documentation

_I_d_e_n_t_i_f_y _m_a_r_k_e_r_s _w_i_t_h _s_w_i_t_c_h_e_d _a_l_l_e_l_e_s

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

     Identify markers whose alleles might have been switched by
     comparing the LOD score for linkage to all other autosomal markers
     with the original data to that when the alleles have been
     switched.

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

     checkAlleles(cross, threshold=3, verbose)

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

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

threshold: Only an increase in maximum 2-point LOD of at least this
          amount will lead to a marker being flagged.

 verbose: If TRUE and there are no markers above the threshold, print a
          message.

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

     For each marker, we compare the maximum LOD score for the cases
     where the estimated recombination fraction > 0.5 to those where
     r.f. < 0.5. The function 'est.rf' must first be run.

     *Note*: Markers that are tightly linked to a marker whose alleles
     are switched are likely to also be flagged by this method.  The
     real problem markers are likely those with the biggest difference
     in LOD scores.

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

     A data frame containing the flagged markers, having four columns:
     the marker name, chromosome ID, numeric index within chromosome,
     and the difference between the maximum two-point LOD score with
     the alleles switched to that from the original data.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'est.rf', 'geno.table'

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

     data(fake.f2)

     # switch homozygotes at marker D5M391
     g <- fake.f2$geno[[5]]$data[,3]
     g <- 4 - g
     fake.f2$geno[[5]]$data[,3] <- g

     fake.f2 <- est.rf(fake.f2)
     checkAlleles(fake.f2)

