ripple                  package:qtl                  R Documentation

_C_o_m_p_a_r_e _m_a_r_k_e_r _o_r_d_e_r_s

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

     Investigate different marker orders for a given chromosome,
     comparing all possible permutations of a sliding window of
     markers.

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

     ripple(cross, chr, window=4, error.prob=0,
            map.function=c("haldane","kosambi","c-f"),
            maxit=1000, tol=1e-5, 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.

  window: Number of markers to include in the sliding window of
          permuted markers.  Larger numbers result in the comparison of
          a greater number of marker orders, but will require a
          considerable increase in computation time.

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 or
          Carter-Falconer 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.

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

     Calculations are done by first constructing a matrix of marker
     orders and then making repeated calls to the R function `est.map'.
      Of course, it would be faster to do everything within C, but this
     was a lot easier to code.

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

     A matrix, given class "ripple"; the first set of columns are
     marker indices describing the order.  The last two columns are lod
     (log base 10 likelihood ratios) comparing each order to the
     initial order and the estimated chromosome length for the given
     order.

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

     Karl W Broman, kbroman@jhsph.edu 
     <URL:
     http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html>

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

     `summary.ripple', `est.map', `est.rf'

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

     data(fake.f2)
     output <- ripple(fake.f2,7,2)
     summary(output,2)

