compareorder               package:qtl               R Documentation

_C_o_m_p_a_r_e _t_w_o _o_r_d_e_r_i_n_g_s _o_f _m_a_r_k_e_r_s _o_n _a _c_h_r_o_m_o_s_o_m_e

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

     Compare the likelihood of an alternative order for markers on a
     chromosome to the current order.

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

     compareorder(cross, chr, order, error.prob=0.0001, 
                  map.function=c("haldane","kosambi","c-f","morgan"),
                  maxit=4000, tol=1e-4, sex.sp=TRUE)

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

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

     chr: The chromosome to investigate.  Only one chromosome is
          allowed. (This should be a character string referring to the
          chromosomes by name.)

   order: The alternate order of markers on the chromosome: a numeric
          vector that is a permutation of the integers from 1 to the
          number of markers on the chromosome.

error.prob: Assumed genotyping error rate used in the calculation of
          the penetrance Pr(observed genotype | true genotype).

map.function: Indicates whether to use the Haldane, Kosambi,
          Carter-Falconer, or Morgan map function when converting
          genetic distances into recombination fractions.

   maxit: Maximum number of EM iterations to perform.

     tol: Tolerance for determining convergence.

  sex.sp: Indicates whether to estimate sex-specific maps; this is 
          used only for the 4-way cross.

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

     A data frame with two rows: the current order in the input cross
     object, and the revised order.  The first column is the log10
     likelihood of the new order relative to the original one (positive
     values indicate that the new order is better supported).  The
     second column is the estimated genetic length of the chromosome
     for each order.   In the case of sex-specific maps, there are
     separate columns for the female and male genetic lengths.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'ripple', 'switch.order', 'move.marker'

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

     data(badorder)
     compareorder(badorder, chr=1, order=c(1:8,11,10,9,12))

